EP4097245A1 - Procédés de prédiction de la réactivité à l'ixabépilone chez des patients atteints d'un cancer - Google Patents

Procédés de prédiction de la réactivité à l'ixabépilone chez des patients atteints d'un cancer

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Publication number
EP4097245A1
EP4097245A1 EP21702662.4A EP21702662A EP4097245A1 EP 4097245 A1 EP4097245 A1 EP 4097245A1 EP 21702662 A EP21702662 A EP 21702662A EP 4097245 A1 EP4097245 A1 EP 4097245A1
Authority
EP
European Patent Office
Prior art keywords
seq
ixabepilone
pharmaceutically acceptable
cancer
acceptable salt
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
Application number
EP21702662.4A
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German (de)
English (en)
Inventor
Steen Knudsen
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Allarity Therapeutics Europe ApS
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Allarity Therapeutics Europe ApS
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Publication date
Application filed by Allarity Therapeutics Europe ApS filed Critical Allarity Therapeutics Europe ApS
Publication of EP4097245A1 publication Critical patent/EP4097245A1/fr
Pending legal-status Critical Current

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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/41—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with two or more ring hetero atoms, at least one of which being nitrogen, e.g. tetrazole
    • A61K31/425—Thiazoles
    • A61K31/427—Thiazoles not condensed and containing further heterocyclic rings
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7042—Compounds having saccharide radicals and heterocyclic rings
    • A61K31/7052—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides
    • A61K31/706—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom
    • A61K31/7064—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines
    • A61K31/7068—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines having oxo groups directly attached to the pyrimidine ring, e.g. cytidine, cytidylic acid
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6851—Quantitative amplification
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers

Definitions

  • biomarkers to predict the responsiveness of a cancer in a subject to a cancer therapy.
  • DNA microarrays have been used to measure gene expression in tumor samples from patients and to facilitate diagnosis. Gene expression can reveal the presence of cancer in a patient in addition to the type, stage, and origin. Gene expression may even have a role in predicting the efficacy of cancer therapies.
  • NCI National Cancer Institute
  • the NCI has tested cancer therapeutics for their effect in limiting the growth of 60 human cancer cell lines. The NCI has also measured gene expression in those 60 cancer cell lines using DNA microarrays.
  • Various studies have explored the relationship between gene expression and therapeutic effect using the NCI datasets.
  • Featured are methods for detecting gene expression of a biomarker e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or2, such as HLA- DRA (SEQ ID NO: 1) and/or PLK2 (SEQ ID NO: 47), respectively, in a patient, such as a patient with a cancer (e.g., a patient with breast cancer or a recurrence thereof) to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a biomarker e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or2, such as HLA- DRA (SEQ ID NO: 1) and/or PLK2 (SEQ ID NO: 47), respectively, in a patient, such as a patient with a cancer (e.g., a patient with breast cancer or a recur
  • Also featured are methods of treating cancer in a patient in need thereof e.g., a patient with breast cancer or a recurrence thereof
  • methods of treating cancer in a patient in need thereof that include administering ixabepilone or a pharmaceutically acceptable salt thereof to the patient, in which the patient is or has been determined to be responsive to ixabepilone or a pharmaceutically acceptable salt thereof according to the diagnostic methods described herein.
  • Exemplary types of cancer that can be diagnosed or treated with the methods include, e.g., breast cancer (e.g., estrogen receptor-positive (ER pos) breast cancer, metastatic form of breast cancer, or medullary carcinoma), ER-positive cancer, endometrial cancer (e.g., FGFR2-mutated or FGFR2-non- mutated advanced or metastatic endometrial cancer), renal cell carcinoma (RCC), hepatocellular carcinoma (HCC), gastrointestinal stromal tumor (GIST), lung cancer (e.g., non-small cell lung carcinoma, large cell carcinoma, bronchogenic carcinoma, and papillary adenocarcinoma), myeloma (e.g., multiple myeloma), colorectal cancer (e.g., colon cancer and rectal cancer), leukemia (e.g., acute myeloid leukemia, acute lymphoid leukemia, chronic myeloid leukemia, chronic lymphocytic leukemia, acute myeloblastic leuk
  • a first aspect features a method of determining responsiveness of a patient with a cancer (e.g., one of the cancers noted above, such as breast cancer) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cancer e.g., one of the cancers noted above, such as breast cancer
  • the patient may have recurrence of cancer, such as recurrence of breast cancer.
  • the method includes: (a) contacting a sample (e.g., a tumor sample) from the patient including one or more nucleic acid molecules with a device (e.g., a microarray, such as a deoxyribonucleic acid (DNA)-based platform) including: (i) one or more single-stranded nucleic acid molecules capable of specifically hybridizing with the nucleotides of one or more biomarkers of sensitivity selected from the biomarkers of Table 1 (e.g., HLA-DRA (SEQ ID NO: 1)); and/or (ii) one or more single-stranded nucleic acid molecules capable of specifically hybridizing with the nucleotides of one or more biomarkers of resistance selected from the biomarkers of Table 2 (e.g., PLK2 (SEQ ID NO: 47)); and (b) measuring hybridization between the one or more nucleic acid molecules from the patient and the single-stranded nucleic acid molecules of the device to detect a level of expression of the one or more bio
  • the patient is determined to be responsive to ixabepilone or a pharmaceutically acceptable salt thereof if: (i) the level of expression of the biomarker(s) of sensitivity (e.g., HLA-DRA (SEQ ID NO: 1)) is substantially similar to the level of expression of the biomarker(s) of sensitivity in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive to ixabepilone or a pharmaceutically acceptable salt thereof (e.g., a tumor sample from a reference subject having the same diagnosis as the patient and that has been determined to be responsive to ixabepilone or a pharmaceutically acceptable salt thereof); (ii) the level of expression of the biomarker(s) of resistance (e.g., PLK2 (SEQ ID NO: 47)) is substantially similar to the level of expression of the biomarker(s) of resistance in a cell (e.g., a cancer cell) or tissue (e.g.,
  • a patient may be deemed sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the expression level of the biomarker(s) of sensitivity in a sample is above a cutoff value of the 50 th percentile in a cell or tissue obtained from a reference subject in a reference population known to be responsive to ixabepilone and having the same diagnosis as the patient, or greater (e.g., 60 th percentile, 70 th percentile, 80 th percentile, or 90 th percentile, or greater).
  • a patient may be deemed sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the expression level of the biomarker(s) of resistance in a cell is above a cutoff value of the 50 th percentile in a cell or tissue obtained from a reference subject in a reference population known to be resistant to ixabepilone and having the same diagnosis as the patient, or greater (e.g., 60 th percentile, 70 th percentile, 80 th percentile, or 90 th percentile, or greater).
  • a patient may be deemed sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the expression level of the biomarker(s) of sensitivity in a cell is below a cutoff value of the 50 th percentile in a cell or tissue obtained from a reference subject in a reference population resistant to ixabepilone treatment and having the same diagnosis as the patient, or less (e.g., 40 th percentile, 30 th percentile, 20 th percentile, or 10 th percentile, or less).
  • a patient may be deemed sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the expression level of the biomarker(s) of resistance in a cell is below a cutoff value of the 50 th percentile in a cell or tissue obtained from a reference subject in a reference population known to be resistant to ixabepilone and having the same diagnosis as the patient, or less (e.g., 40 th percentile, 300 th percentile, 20 th percentile, or 100 th percentile, or less).
  • Responsiveness of the patient to ixabepilone or a pharmaceutically acceptable salt thereof can also be assessed by calculating a difference score for the patient (mean of expression of the biomarkers of sensitivity noted above minus the mean of expression of the biomarkers of resistance noted above).
  • the method of the first aspect can further include administering ixabepilone or a pharmaceutically acceptable salt thereof to the patient having: (i) a level of expression of the biomarker(s) of sensitivity (e.g., HLA-DRA (SEQ ID NO: 1)) that is substantially similarto the level of expression of the biomarker(s) of sensitivity in a cell (e.g., a cancer cell) or tissue (e.g., a tumortissue) known to be sensitive to ixabepilone or a pharmaceutically acceptable salt thereof; (ii) a level of expression of the biomarker(s) of resistance (e.g., PLK2 (SEQ ID NO: 47)) that is substantially similarto the level of expression of the biomarker(s) of resistance in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive to ixabepilone or a pharmaceutically acceptable salt thereof; (iii) a level of expression
  • the method can further include administering one or more cancer therapies other than ixabepilone or a pharmaceutically acceptable salt thereof to the patient having: (i) a level of expression of the biomarker(s) of sensitivity (e.g., HLA-DRA (SEQ ID NO: 1)) that is substantially dissimilarto the level of expression of the biomarker(s) of sensitivity in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive to ixabepilone or a pharmaceutically acceptable salt thereof; (ii) a level of expression of the biomarker(s) of resistance (e.g., PLK2 (SEQ ID NO: 47)) that is substantially dissimilar to the level of expression of the biomarker(s) of resistance in a cell (e.g., a cancer cell) or tissue (e.g., a tumortissue) known to be sensitive to ixabepilone or a pharmaceutically acceptable salt thereof; (iii)
  • the one or more cancer therapies can include surgery, radiation, or a therapeutic agent, such as capecitabine, a histone deacetylase (HDAC) inhibitor, an immune checkpoint inhibitor (e.g., a PD1 inhibitor, a PD-L1 inhibitor, or a CTLA-4 inhibitor), ipilimumab, a cyclin-dependent kinase inhibitor (e.g., a CDK inhibitor selective for CDK4 and CDK6, such as palbociclib (IBRANCE®) and abemaciclib (VERZENIO®, VERZENIOS®)), venetoclax (VENCLEXTA®, VENCLYXTO®), ibrutinib (IMBRUVICA®), bortezomib, carfilzomib, thalidomide, lenalidomide, pomalidomide, prednisone, dexamethasone, cyclophosphamide, vincristine, doxorubicin
  • Also featured is a method of treating cancer in a patient in need thereof e.g., a patient with one of the cancers noted above, such as breast cancer, that includes administering ixabepilone or a pharmaceutically acceptable salt thereof to the patient, in which the patient has been determined to be responsive to ixabepilone or a pharmaceutically acceptable salt thereof according to the method of the first aspect of the invention.
  • the patient may have recurrence of cancer, such as recurrence of breast cancer.
  • a second aspect features a method of treating a patient having cancer (e.g., one of the cancers noted above, such as breast cancer).
  • the patient may have recurrence of cancer, such as recurrence of breast cancer.
  • the method includes: (a) contacting a sample (e.g., a tumor sample) from the patient including one or more nucleic acid molecules with a device including: (i) one or more single- stranded nucleic acid molecules capable of specifically hybridizing with the nucleotides of one or more biomarkers of sensitivity selected from the biomarkers of Table 1 (e.g., HLA-DRA (SEQ ID NO: 1)); and/or (ii) one or more single-stranded nucleic acid molecules capable of specifically hybridizing with the nucleotides of one or more biomarkers of resistance selected from the biomarkers of Table 2 (e.g., PLK2 (SEQ ID NO: 47)); (b) measuring hybridization between the one or more nucleic acid molecules from the
  • Ixabepilone or a pharmaceutically acceptable salt thereof can be administered to the patient if: (i) the level of expression of the biomarker(s) of sensitivity (e.g., HLA-DRA (SEQ ID NO: 1)) is substantially similar to the level of expression of the biomarker(s) of sensitivity in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive to ixabepilone or a pharmaceutically acceptable salt thereof; (ii) the level of expression of the biomarker(s) of resistance (e.g., PLK2 (SEQ ID NO: 47)) is substantially similarto the level of expression of the biomarker(s) of resistance in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive to ixabepilone or a pharmaceutically acceptable salt thereof; (iii) the level of expression of the biomarker(s) of sensitivity (e
  • the method of the foregoing aspects may further include administering one or more additional therapies (e.g., surgery, radiation, or a therapeutic agent) to the patient prior to, concurrently with, or after administration of ixabepilone or a pharmaceutically acceptable salt thereof.
  • additional therapies e.g., surgery, radiation, or a therapeutic agent
  • a therapeutic agent that is administered to the patient prior to, concurrently with, or after administration of ixabepilone or a pharmaceutically acceptable salt thereof is capecitabine.
  • a therapeutic agent that is administered to the patient prior to, concurrently with, or after administration of ixabepilone or a pharmaceutically acceptable salt thereof is capecitabine.
  • a therapeutic agent that is administered to the patient prior to, concurrently with, or after administration of ixabepilone or a pharmaceutically acceptable salt thereof is one or more of capecitabine, an HDAC inhibitor, an immune checkpoint inhibitor (e.g., a PD1 inhibitor (e.g., Pembrolizumab, Nivolumab, and Cemiplimab), a PD-L1 inhibitor (e.g., Atezolizumab, Avelumab, and Durvalumab), and a CTLA-4 inhibitor (e.g., Ipilimumab, and Tremelimumab)), an aromatase inhibitor (e.g., a non-selective aromatase inhibitor, such as Aminoglutethimide and Testolactone; a selective aromatase inhibitor, such as anastrozole, letrozole, exemestane, vorozole, formestane, and fadrozole; and other organic organ
  • the therapeutic agent can be administered parenterally (e.g. intravenously, intramuscularly, transdermally, intradermally, intra-arterially, intracranially, subcutaneously, intraorbitally, intraventricularly, intraspinally, intraperitoneally, or intranasally), enterally, or topically.
  • the method of any of the foregoing aspects includes administering capecitabine to the subject two or more times.
  • the method of any of the foregoing aspects includes administering capecitabine to the subject one or more times daily, weekly, every two weeks, every three weeks, or monthly.
  • the capecitabine is administered two times per day.
  • the method includes administering capecitabine to the subject one or more times every three weeks.
  • the capecitabine is administered to the subject two times per day on days 1-14 of a three-week treatment cycle.
  • the capecitabine is administered to the subject at a dose of 1000 mg/m 2 .
  • the capecitabine is administered to the subject at a dose of about 2000-2500 mg (e.g., 2000 mg, 2100 mg, 2200 mg, 2300 mg, 2400 mg, 2500 mg).
  • the capecitabine is administered to the subject at a dose of 2000 mg.
  • the capecitabine is administered as an intravenous infusion or injection.
  • the capecitabine is administered to the subject as an intravenous infusion containing capecitabine at a dose of 1000 mg/m 2 two times per day on days 1-14 of a three-week treatment cycle.
  • ixabepilone or a pharmaceutically acceptable salt thereof may be administered parenterally (e.g. intravenously, intramuscularly, transdermally, intradermally, intraarterially, intracranially, subcutaneously, intraorbitally, intraventricularly, intraspinally, intraperitoneally, or intranasally), enterally (e.g., orally), or topically.
  • parenterally e.g. intravenously, intramuscularly, transdermally, intradermally, intraarterially, intracranially, subcutaneously, intraorbitally, intraventricularly, intraspinally, intraperitoneally, or intranasally
  • enterally e.g., orally
  • ixabepilone or a pharmaceutically acceptable salt thereof is administered as an intravenous infusion or injection.
  • Ixabepilone or a pharmaceutically acceptable salt thereof may be administered to the patient one or more times, such as one or more times daily (e.g., once daily for up to six days), weekly, every two weeks, every three weeks, or monthly.
  • ixabepilone or a pharmaceutically acceptable salt thereof is administered one or more times every three weeks.
  • ixabepilone or a pharmaceutically acceptable salt thereof is administered once every three weeks.
  • the ixabepilone or a pharmaceutically acceptable salt thereof is administered on day one of a three-week treatment cycle.
  • the method may further include administering a second dose of ixabepilone or a pharmaceutically acceptable salt thereof to the subject (e.g., patient) two days, four days, six days, one week, two weeks, three weeks, four weeks, or five weeks after administration of a first dose of ixabepilone or a pharmaceutically acceptable salt thereof.
  • Ixabepilone or a pharmaceutically acceptable salt thereof may be administered in a particular dosage form (e.g., intravenous infusion or injection).
  • the dose administered may be about 40 mg/m 2 (e.g., 40 mg/m 2 ).
  • ixabepilone or a pharmaceutically acceptable salt thereof may be administered at a dose(s) of about 40-120 mg (e.g., about 40 mg, 50 mg, 60 mg, 70 mg, 80 mg, 90 mg, 100 mg, 110 mg, or 120 mg).
  • ixabepilone or a pharmaceutically acceptable salt thereof may be administered at a dose of 80 mg.
  • ixabepilone or a pharmaceutically acceptable salt thereof is administered to the subject on day one of a three-week treatment cycle at a dose at or about 40 mg/m 2 delivered as an intravenous infusion or injection.
  • the ixabepilone or a pharmaceutically acceptable salt thereof is formulated for administration as a solution comprising ixabepilone at a concentration of at or about 0.2 img/mL to 0.6 mg/mL.
  • the contacting step (a) and the measuring step (b) may occur prior to, concurrent to, or after administration of ixabepilone or a pharmaceutically acceptable salt thereof to the patient.
  • Each of the contacting step (a) and the measuring step (b) may occur multiple times.
  • the device e.g., a microarray, such as a DNA-based platform
  • the device can include at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, or more single-stranded nucleic acid molecules capable of specifically hybridizing with the nucleotides of one or more biomarkers of sensitivity selected from the biomarkers of Table 1 (e.g., HLA-DRA (SEQ ID NO: 1)); and/or at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, or more single-stranded nucleic acid molecules capable of specifically hybridizing with the nucleotides of one or more biomarkers of resistance selected from the biomarkers of Table 2 (e.g., PLK2 (SEQ ID NO: 47)).
  • the device may have single- stranded nucleic acid molecule(s) having the sequence of or complementary to each of the biomarkers of sensitivity selected from the biomarkers of Table 1 and for each of the biomarkers of resistance selected from the biomarkers of Table 2 that are affixed to the device and can be used to detect the level of expression of the biomarkers, e.g., by hybridization.
  • one or more of the single-stranded nucleic acid molecules of the device have a length in the range of 10 to 100 nucleotides in length (e.g., a length in the range of 20 to 60 nucleotides).
  • the method may include converting the level of expression of one or more of the biomarkers of sensitivity (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Table 1 (e.g., the top one biomarker, the top two biomarkers, the top three biomarkers, the top four biomarkers, the top five biomarkers, the top ten biomarkers, the top fifteen biomarkers, the top twenty biomarkers, the top twenty five biomarkers, or all of the biomarkers shown in Table 1), such as HLA-DRA (SEQ ID NO: 1)) and/or one or more of the biomarkers of resistance (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Table 2 (e.g., the top one biomarker, the top two biomarkers, the top three biomarkers, the top four biomarkers, the top five biomarkers,
  • the method can further include subtracting the mean score for one or more of the biomarkers of resistance (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Table 2 (e.g., the top one biomarker, the top two biomarkers, the top three biomarkers, the top four biomarkers, the top five biomarkers, the top ten biomarkers, the top fifteen biomarkers, the top twenty biomarkers, the top twenty five biomarkers, or all of the biomarkers shown in Table 2), such as PLK2 (SEQ ID NO: 47)) from the mean score for one or more of the biomarkers of sensitivity (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Table 1 (e.g., the top one biomarker, the top two biomarkers, the top three biomarkers, the top four biomarkers, the top five biomarkers, the top ten bio
  • the mean score and/or the difference score of the biomarkers from a subject can be compared to the mean scores or difference scores of the biomarkers obtained from a reference population of tumor samples of the same type (e.g., from subjects diagnosed with the same type of tumor), in which the mean score or difference score of the biomarkers obtained from the subject falling at or above the 50 th percentile of the reference population, or the 60 th percentile, or the 70 th percentile, or the 80 th percentile, or the 90 th percentile, or greater, can be used to predict the likelihood that a tumor (or a subject from whom the tumor sample is taken) will be responsive to a treatment (e.g., treatment with ixabepilone or a pharmaceutically acceptable salt thereof).
  • a treatment e.g., treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a mean score or difference score of the biomarkers obtained from the subject that falls below the 50 th percentile of the reference population can be used to predict the likelihood that a tumor (or a subject from whom the tumor sample is taken) will be non-responsive to a treatment (e.g., treatment with ixabepilone or a pharmaceutically acceptable salt thereof).
  • a treatment e.g., treatment with ixabepilone or a pharmaceutically acceptable salt thereof
  • an expression level (or the mean score and/or the difference score thereof) of a sample e.g., a tumor sample from a subject
  • the 60 th percentile, or the 70 th percentile, or the 80 th percentile, or the 90 th percentile, or greater indicates that the sample (or the subject from whom the sample was taken) is predicted to be responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • the confidence of the prediction increases as the percentile level increases (e.g., an expression level above the 90 th percentile of a reference population indicates a greater likelihood of treatment responsiveness than an expression level at the 50 th percentile). Conversely, an expression level in the tested sample of below the 50 th percentile of the reference population indicates that the sample (or the subject from whom the sample was taken) is predicted to be non-responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • the device can be a microarray, such as a DNA-based platform.
  • the expression level of the biomarkers of sensitivity e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Table 1 (e.g., the top one biomarker, the top two biomarkers, the top three biomarkers, the top four biomarkers, the top five biomarkers, the top ten biomarkers, the top fifteen biomarkers, the top twenty biomarkers, the top twenty five biomarkers, or all of the biomarkers shown in Table 1), such as HLA-DRA (SEQ ID NO: 1)) and/or the biomarkers of resistance (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Table 2 (e.g., the top one biomarker, the top two biomarkers, the top three biomarkers, the top four biomarkers, the top five biomarkers, the top ten biomarkers, the top fifteen biomarkers, the top twenty biomarkers
  • the biomarker of sensitivity may be selected from one or more of HLA-DRA (SEQ ID NOs: 1 and 2), ICA 3 (SEQ ID NO: 3), ITGB7 (SEQ ID NO: 4), CD8B (SEQ ID NO: 5), CD74 (SEQ ID NO: 6), HLA-DRB1 HLA-DRB4 HLA-DRB5 LOC100507709 LOC100507714 (SEQ ID NO: 7), IGJ (SEQ ID NO: 8), HLA-DRB1 HLA-DRB3 HLA-DRB4 LOC100507709 LOC100507714 (SEQ ID NO: 9), HLA-DPA1 (SEQ ID NOs: 10 and 12), HLA-DRB1 LOC100507709 LOC100507714 (SEQ ID NO: 11), CD28 (SEQ ID NO: 13), CD37 (SEQ ID NO: 14), NHP2 (SEQ ID NO: 15), MZB1 (SEQ ID NO: 16), AD
  • the biomarker of resistance may be selected from one or more of PLK2 (SEQ ID NO: 47), PLXNB2 (SEQ ID NO: 48), RRAS2 (SEQ ID NO: 49 and 50), PTPLA (SEQ ID NO: 51), P2RX5-TAX1 BP3 TAX1 BP3 (SEQ ID NO: 52), STAT3 (SEQ ID NO: 53), PPIC (SEQ ID NO:
  • PTRF SEQ ID NO: 55
  • RCN1 SEQ ID NO: 56
  • ZFP36L1 SEQ ID NO: 57
  • GFPT1 SEQ ID NO: 58 AND 112
  • ACTN1 SEQ ID NOs: 59 and 61
  • SEPT10 SEQ ID NO: 60
  • COL4A1 SEQ ID NO: 62
  • ERBB2IP SEQ ID NO: 63
  • NNMT SEQ ID NOs: 64 and 66
  • ADAM9 SEQ ID NO: 65
  • TOR1AIP1 SEQ ID NO: 67
  • ATP1 B1 SEQ ID NO: 68
  • CEBPD SEQ ID NO: 69
  • FLII SEQ ID NO: 70
  • FHL2 SEQ ID NO: 71
  • SHC1 SEQ ID NO: 72
  • SPTAN1 SEQ ID NO: 73
  • CD81 SEQ ID NO: 74
  • IQGAP1 SEQ ID NO: 75
  • TGIF1 SEQ ID NO:
  • the biomarkers of sensitivity may include one or more of: (a) SEQ ID NOs: 1-15.
  • the biomarker of sensitivity may be HLA-DRA (SEQ ID NO:
  • the biomarkers of resistance may include one or more of: (a) SEQ ID NOs: 47-62.
  • the biomarker of resistance may be PLK2 (SEQ ID NO: 47).
  • the biomarker of sensitivity may be HLA-DRA (e g., SEQ ID NO: 1) and the biomarker of resistance may be PLK2 (e.g., SEQ ID NO: 47).
  • the biomarkers of sensitivity may be selected from at least 5, at least 10, at least 15, at least 20, at least 25, or at least 27 of the biomarkers of Table 1 (e.g., at least the top 5 biomarkers, at least the top 10 biomarkers, at least the top 15 biomarkers, at least the top 20 biomarkers, at least the top 25 biomarkers, or at least the top 27 biomarkers of Table 1).
  • the biomarkers of resistance may be selected from at least 5, at least 10, at least 15, at least 20, at least 25, or at least 27 of the biomarkers of Table 2 (e.g., at least the top 5 biomarkers, at least the top 10 biomarkers, at least the top 15 biomarkers, at least the top 20 biomarkers, at least the top 25 biomarkers, or at least the top 27 biomarkers of Table 2).
  • the cancer is selected from a solid tumor cancer and a hematological cancer.
  • the cancer is, e.g., breast cancer, multiple myeloma, acute myelogenous leukemia (AML), acute lympho-blastic leukemia (ALL), chronic lymphocytic leukemia (CLL), myelodysplastic syndrome (MDS), chronic myelogenous leukemia - chronic phase (CMLCP), diffuse large B-cell lymphoma (DLBCL), cutaneous T-cell lymphoma (CTCL), peripheral T-cell lymphoma (PTCL), Hodgkin's lymphoma, hepatocellular carcinoma (HCC), cervical cancer, prostate cancer, kidney cancer, renal cell carcinoma (RCC), esophageal cancer, melanoma, glioma, pancreatic cancer, ovarian cancer, gastrointestinal stromal tumors (GIST), sarcoma, breast cancer, estrogen receptor-positive (ERpos) breast cancer, meta
  • AML acute mye
  • ixabepilone As used herein, the terms “ixabepilone,” “azaepothilone B,” and “BMS-247550” refer to (1 S,3S,7S,10R,11S,12S,16R)-7,11 dihydroxy-8, 8, 10, 12, 16-pentamethyl-3-[(1 E)-1-methyl-2-(2-methyl-4- thiazolyl)ethenyl] 17-oxa-4-azabicyclo[14.1.0] heptadecane-5,9-dione or a tautomer thereof, or a mixture of tautomers thereof.
  • Ixabepilone is a semi-synthetic analog of epothilone B that directly binds to b- tubulin monomers of microtubules and reduces microtubule disassembly.
  • This microtubule-stabilizing property of ixabepilone renders it a potent anti-tumor agent by creating defects in mitotic spindle assembly, chromosome segregation, and cell division, thereby inhibiting the progression of mitosis and ultimately triggering apoptosis or reversion to the GO-phase of the cell cycle without cell division.
  • ixabepilone may refer to a pharmaceutically acceptable salt thereof.
  • Ixabepilone has the following structure: Exemplary methods of preparing ixabepilone are described in detail in US 2002/0188014 and US 2003/0004338, the disclosures of which are incorporated herein in their entirety.
  • the ixabepilone or a pharmaceutically acceptable salt disclosed herein can have one or more asymmetric carbon atoms and can exist in the form of optically pure enantiomers, mixtures of enantiomers such as, for example, racemates, optically pure diastereoisomers, mixtures of diastereoisomers, diastereoisomeric racemates, or mixtures of diastereoisomeric racemates.
  • the optically active forms can be obtained for example by resolution of the racemates, by asymmetric synthesis or asymmetric chromatography (chromatography with a chiral adsorbent or eluant). That is, ixabepilone or a pharmaceutically acceptable salt thereof may exist in various stereoisomeric forms.
  • Stereoisomers are compounds that differ only in their spatial arrangement. Enantiomers are pairs of stereoisomers whose mirror images are not superimposable, most commonly because they contain an asymmetrically substituted carbon atom that acts as a chiral center. "Enantiomer” means one of a pair of molecules that are mirror images of each other and are not superimposable. Diastereomers are stereoisomers that are not related as mirror images, most commonly because they contain two or more asymmetrically substituted carbon atoms and represent the configuration of substituents around one or more chiral carbon atoms.
  • Enantiomers of ixabepilone or a pharmaceutically acceptable salt can be prepared, for example, by separating an enantiomer from a racemate using one or more well-known techniques and methods, such as, for example, chiral chromatography and separation methods based thereon.
  • the appropriate technique and/or method for separating an enantiomer of a compound described herein from a racemic mixture can be readily determined by those of skill in the art.
  • Racemate or “racemic mixture” means a compound containing two enantiomers, wherein such mixtures exhibit no optical activity; i.e., they do not rotate the plane of polarized light.
  • “Geometric isomer” means isomers that differ in the orientation of substituent atoms in relationship to a carbon-carbon double bond, to a cycloalkyl ring, or to a bridged bicyclic system. Atoms (other than H) on each side of a carbon- carbon double bond may be in an E (substituents are on 25 opposite sides of the carbon- carbon double bond) orZ (substituents are oriented on the same side) configuration. "R,” “S,” “S*,” “R*,” “E,” “Z,” “cis,” and “trans,” indicate configurations relative to the core molecule. Certain of the disclosed compounds may exist in atropisomeric forms.
  • Atropisomers are stereoisomers resulting from hindered rotation about single bonds where the steric strain barrier to rotation is high enough to allow for the isolation of the conformers.
  • the ixabepilone or a pharmaceutically acceptable salt thereof herein may be prepared as individual isomers by either isomer-specific synthesis or resolved from an isomeric mixture.
  • Conventional resolution techniques include forming the salt of a free base of each isomer of an isomeric pair using an optically active acid (followed by fractional crystallization and regeneration of the free base), forming the salt of the acid form of each isomer of an isomeric pair using an optically active amine (followed by fractional crystallization and regeneration of the free acid), forming an ester or amide of each of the isomers of an isomeric pair using an optically pure acid, amine or alcohol (followed by chromatographic separation and removal of the chiral auxiliary), or resolving an isomeric mixture of either a starting material or a final product using various well known chromatographic methods.
  • the stereochemistry of a disclosed compound is named or depicted by structure
  • the named or depicted stereoisomer is at least 60%, 70%, 80%, 90%, 99%, or 99.9% by weight relative to the other stereoisomers.
  • the depicted or named enantiomer is at least 60%, 70%, 80%, 90%, 99%, or 99.9% by weight optically pure.
  • the depicted or named diastereomer is at least 60%, 70%, 80%, 90%, 99%, or 99.9% by weight pure.
  • Percent optical purity is the ratio of the weight of the enantiomer or over the weight of the enantiomer plus the weight of its optical isomer. Diastereomeric purity by weight is the ratio of the weight of one diastereomer or over the weight of all the diastereomers.
  • the stereochemistry of ixabepilone or a pharmaceutically acceptable salt thereof is named or depicted by structure, the named or depicted stereoisomer is at least 60%, 70%, 80%, 90%, 99%, or 99.9% by mole fraction pure relative to the other stereoisomers.
  • the depicted or named enantiomer is at least 60%, 70%, 80%, 90%,
  • ixabepilone or a pharmaceutically acceptable salt thereof is named or depicted by structure without indicating the stereochemistry, and the ixabepilone or a pharmaceutically acceptable salt thereof has at least one chiral center, it is to be understood that the name or structure encompasses either enantiomer of the ixabepilone or a pharmaceutically acceptable salt thereof free from the corresponding optical isomer, a racemic mixture of the ixabepilone or a pharmaceutically acceptable salt thereof, or mixtures enriched in one enantiomer relative to its corresponding optical isomer.
  • ixabepilone or a pharmaceutically acceptable salt thereof is named or depicted by structure without indicating the stereochemistry and has two or more chiral centers, it is to be understood that the name or structure encompasses a diastereomer free of other diastereomers, a number of diastereomers free from other diastereomeric pairs, mixtures of diastereomers, mixtures of diastereomeric pairs, mixtures of diastereomers in which one diastereomer is enriched relative to the other diastereomer(s), or mixtures of diastereomers in which one or more diastereomer is enriched relative to the other diastereomers.
  • the invention embraces all of these forms.
  • biomarker is meant a nucleic acid molecule (e.g., an mRNA or its complement, for example, a cDNA) or a protein encoded by the nucleic acid molecule present in, or from, a cell or tissue (e.g., tumor tissue).
  • a cell or tissue e.g., tumor tissue.
  • the expression of the biomarker correlates to the responsiveness (e.g., sensitivity or resistance) of the cell or tissue (and thus, the patient containing the cell or tissue or the patient from which the cell or tissue was obtained) to a cancer treatment (e.g., ixabepilone or a pharmaceutically acceptable salt thereof).
  • a biomarker of sensitivity is a nucleic acid molecule (e.g., a mRNA or its complement) expressed from any one of the genes shown in Table 1 , or the protein encoded by the nucleic acid molecule
  • a biomarker of resistance is a nucleic acid molecule (e.g., a mRNA or its complement) expressed from any one of the genes shown in Table 2, or the protein encoded by the nucleic acid molecule.
  • cancer refers to or describe the physiological condition in mammals (e.g., humans) that is typically characterized by unregulated cell proliferation.
  • examples of cancer include, but are not limited to, breast cancer (e.g., medullary carcinoma), myeloma (e.g., multiple myeloma), colorectal cancer (e.g., colon cancer and rectal cancer), leukemia (e.g., acute myeloid leukemia, acute lymphoid leukemia, chronic myeloid leukemia, chronic lymphocytic leukemia, acute myeloblastic leukemia, acute promyelocytic leukemia, acute myelomonocytic leukemia, acute monocytic leukemia, acute erythroleukemia, and chronic leukemia), myelodysplastic syndrome, lymphoma (e.g., diffuse large B-cell lymphoma, cutaneous T-cell lymphoma, peripheral T-cell lymphoma, Hodg
  • lymphoma
  • expression level and “level of expression,” as used herein interchangeably, refer to the amount of a gene product in a cell, tissue, biological sample, organism, or patient, e.g., amounts of DNA, RNA (e.g. messenger RNA (mRNA) of), or protein encoded by a given gene.
  • RNA e.g. messenger RNA (mRNA) of
  • protein encoded by a given gene e.g., protein encoded by a given gene.
  • Gene indicates a coding or noncoding gene whose activity can be determined by measuring the produced RNA. Examples include protein coding genes, microRNAs, small nuclear RNAs and other RNAs with catalytic, regulatory or coding properties.
  • inhibit growth means causing a reduction in cell growth (e.g., cancer cell growth, e.g., as compared to the growth inhibition of the NCI60 cancer cell lines as a reference) in vivo or in vitro by, e.g., 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, or 99% or more, as evident by a reduction in the proliferation of cells exposed to a treatment (e.g., ixabepilone or a pharmaceutically acceptable salt thereof), relative to the proliferation of cells in the absence of the treatment.
  • a treatment e.g., ixabepilone or a pharmaceutically acceptable salt thereof
  • Growth inhibition may be the result of a treatment (e.g., ixabepilone or a pharmaceutically acceptable salt thereof) that induces apoptosis in a cell, induces necrosis in a cell, slows cell cycle progression, disrupts cellular metabolism, induces cell lysis, or induces some other mechanism that reduces the proliferation of cells.
  • a treatment e.g., ixabepilone or a pharmaceutically acceptable salt thereof
  • “Microarray” as used herein means a device employed by any method that quantifies one or more subject oligonucleotides, e.g., RNA, DNA, cDNA, or analogues thereof, at a time.
  • DNA microarrays including those made by Affymetrix (e.g., an Affymetrix HG-U133A array), use several probes for determining the expression of a single gene.
  • the DNA microarray may contain oligonucleotide probes that may be, e.g., full-length cDNAs complementary to an RNA or cDNA fragments that hybridize to part of an RNA.
  • the DNA microarray may also contain modified versions of DNA or RNA, such as locked nucleic acids or LNA.
  • Exemplary RNAs include mRNA, miRNA, and miRNA precursors.
  • percent (%) sequence identity refers to the percentage of nucleic acid residues of a candidate sequence, e.g., a probe or primer of the invention, that are identical to the nucleic acid residues of a reference sequence, e.g., a biomarker sequence of the invention, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity (e.g., gaps can be introduced in one or both of the candidate and reference sequences for optimal alignment and non-homologous sequences can be disregarded for comparison purposes).
  • Alignment for purposes of determining percent sequence identity can be achieved in various ways that are within the skill in the art, for instance, using computer software, such as BLAST, BLAST-2, BLAST-P, BLAST-N, BLAST-X, WU-BLAST-2, ALIGN, ALIGN-2, CLUSTAL, Megalign (DNASTAR).
  • computer software such as BLAST, BLAST-2, BLAST-P, BLAST-N, BLAST-X, WU-BLAST-2, ALIGN, ALIGN-2, CLUSTAL, Megalign (DNASTAR).
  • those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve optimal alignment overthe length of the sequences being compared.
  • NCI60 as used herein means a panel of 60 cancer cell lines from lung, colon, breast, ovarian, leukemia, renal, melanoma, prostate and brain cancers including the following cancer cell lines: NSCLC_NCIH23, NSCLC_NCIH522, NSCLC_A549ATCC, NSCLC_EKVX, NSCLC_NCIH226, NSCLC_NCIH332 , NSCLCJH460, NSCLCJHOP62, NSCLCJHOP92, COLONJHT29, COLON JHCC- 2998, COLONJHCT116, COLON_SW620, COLON_COLO205, COLON_HCT15, COLON_KM12, BREAST_MCF7, BREAST_MCF7ADRr, BREAST_MDAMB231 , BREAST_HS578T, BREAST_MDAMB435, BREAST_MDN, BREAST_BT549, BREAST_
  • patient refers to any animal (e.g., a mammal, such as a human).
  • a patient to be treated or tested for responsiveness to a treatment e.g., ixabepilone or a pharmaceutically acceptable salt thereof
  • a treatment e.g., ixabepilone or a pharmaceutically acceptable salt thereof
  • Diagnosis may be performed by any method or techniques known in the art, such as x-ray, MRI, or biopsy, and confirmed by a physician.
  • the patient may be determined to be either responsive or non-responsive to a cancer treatment, such as ixabepilone or a pharmaceutically acceptable salt thereof, according to the methods described herein.
  • the term “pharmaceutically acceptable salt” means any pharmaceutically acceptable salt of the compound of any of the compounds described herein.
  • pharmaceutically acceptable salts of ixabepilone or a pharmaceutically acceptable salt thereof described herein include those that are within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and animals without undue toxicity, irritation, allergic response and are commensurate with a reasonable benefit/risk ratio.
  • Pharmaceutically acceptable salts are well known in the art. For example, pharmaceutically acceptable salts are described in: Berge et al., J. Pharmaceutical Sciences 66:1-19, 1977 and in Pharmaceutical Salts: Properties, Selection, and Use, (Eds. P.H. Stahl and C.G. Wermuth), Wiley-VCH, 2008.
  • the salts can be prepared in situ during the final isolation and purification of the compounds described herein or separately by reacting a free base group with a suitable organic acid.
  • the ixabepilone described herein may have ionizable groups so as to be capable of preparation as pharmaceutically acceptable salts.
  • These salts may be acid addition salts involving inorganic or organic acids or the salts may, in the case of acidic forms of the compounds described herein, be prepared from inorganic or organic bases. Frequently, the compounds are prepared or used as pharmaceutically acceptable salts prepared as addition products of pharmaceutically acceptable acids or bases. Suitable pharmaceutically acceptable acids and bases and methods for preparation of the appropriate salts are well-known in the art. Salts may be prepared from pharmaceutically acceptable non-toxic acids and bases including inorganic and organic acids and bases.
  • Representative acid addition salts include acetate, adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, fumarate, glucoheptonate, glycerophosphate, hemisulfate, heptonate, hexanoate, hydrobromide, hydrochloride, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pe
  • alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, and magnesium, as well as nontoxic ammonium, quaternary ammonium, and amine cations, including, but not limited to ammonium, tetramethylammonium, tetraethylammonium, methylamine, dimethylamine, trimethylamine, triethylamine, and ethylamine.
  • “Resistance” as used herein means that a cell (e.g., a cancer cell) or a tissue (e.g., a tumor) in vitro or in vivo (e.g., in a subject with a cancer, such as a human) is tolerant to treatment with an anticancer agent (e.g., ixabepilone or a pharmaceutically acceptable salt thereof), e.g., the cell or tissue (e.g., tumor tissue) is able to survive and grow despite exposure to (e.g., treatment with) an anti-cancer agent (e.g., ixabepilone or a pharmaceutically acceptable salt thereof).
  • an anticancer agent e.g., ixabepilone or a pharmaceutically acceptable salt thereof
  • Resistance may arise via exploitation by a cell or tissue (e.g., a tumor tissue) of one or more of drug inactivation, drug target alteration, drug efflux, DNA damage repair, cell death inhibition, cell cycle regulation, epithelial- mesenchymal transition (EMT), epigenetics, and other mechanisms.
  • a “resistant” cell or tissue refers to a cell (e.g., a cancer cell) or a tissue (e.g., a tumor), respectively, in vitro or in vivo (e.g., in a subject with a cancer, such as a human) that has acquired and/or exhibits resistance to a treatment (e.g., ixabepilone or a pharmaceutically acceptable salt thereof).
  • a resistant cell or tissue e.g., a tumor tissue
  • a cancer therapeutic e.g., ixabepilone or a pharmaceutically acceptable salt thereof
  • an inhibition in growth of the cell or tumor of less than 30%, 25%, 20%, 15%, 10%, 5%, or 1% relative to the growth of a cell or tissue not exposed to the treatment.
  • Resistance to treatment may be determined by a cell proliferation assay, e.g., a cell-based assay, which measures the growth of treated cells as a function of the absorbance of the cells of an incident light beam, such as the NCI60 assays described herein. In this assay, greater absorbance indicates greater cell growth, and thus, resistance to the treatment.
  • a cell proliferation assay e.g., a cell-based assay, which measures the growth of treated cells as a function of the absorbance of the cells of an incident light beam, such as the NCI60 assays described herein. In this assay, greater absorbance indicates greater cell growth, and thus, resistance to the treatment.
  • sensitivity refers to the likelihood that a cancer treatment (e.g., ixabepilone or a pharmaceutically acceptable salt thereof) has (e.g., induces) a desired effect, or alternatively refers to the strength of a desired effect caused or induced by the treatment in a cell (e.g., a cancer cell) or a tissue (e.g., a tumor) in vitro or in vivo (e.g., in a subject with a cancer, such as a human).
  • a cancer treatment e.g., ixabepilone or a pharmaceutically acceptable salt thereof
  • the desired effect can include inhibition of the growth of a cell (e.g., a cancer cell) in vitro by more than 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%,
  • the desired effect can also include reduction in tumor mass by, e.g., about 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%.
  • “Sensitive” and “responsive” as used herein refer to a cell (e.g., a cancer cell) or a tissue (e.g., a tumor) in vitro or in vivo (e.g., in a subject with a cancer, such as a human) that is responsive to exposure to a therapeutic (e.g., ixabepilone or a pharmaceutically acceptable salt thereof). Responsiveness to treatment may be determined by a cell proliferation assay, e.g., a cell-based assay, which measures the growth of treated cells as a function of the absorbance of the cells of an incident light beam, such as the NCI60 assays described herein. In this assay, lesser absorbance indicates lesser cell growth, and thus, sensitivity or responsiveness to the treatment. A greater reduction in growth indicates more sensitivity or responsiveness to the treatment.
  • a cell proliferation assay e.g., a cell-based assay, which measures the growth of treated cells as a function of the absorbance of the
  • sample refers to any specimen (such as cells, tissue (e.g., a tissue sample obtained by biopsy), blood, serum, plasma, urine, cerebrospinal fluid, or pancreatic fluid) taken from a subject.
  • tissue e.g., a tissue sample obtained by biopsy
  • blood serum, plasma, urine, cerebrospinal fluid, or pancreatic fluid
  • the sample is taken from a portion of the body affected by a cancer (e.g., a biopsy of the cancer tissue).
  • Biopsy may involve fine needle aspiration biopsy, core needle biopsy (e.g., stereotactic core needle biopsy, vacuum-assisted core biopsy, or magnetic resonance imaging (MRI) guided biopsy), or surgical biopsy (e.g., incisional biopsy or excisional biopsy).
  • the sample may undergo additional purification and processing, for example, to remove cell debris and other unwanted molecules. Additional processing may further involve amplification, e.g., using PCR (e.g., RT-PCR).
  • PCR e.g., RT
  • “Substantially similar” or “corresponds,” as used herein with respect to a numerical value of a parameter of one or more of the biomarker(s) of sensitivity and/or resistance e.g., biomarker expression level, difference score, or mean score
  • a test sample e.g., a tumor biopsy
  • the numerical value of the parameter in the test sample is ⁇ 0-30% of the numerical value of the parameter in a reference sample (e.g., a cell (e.g., a cancer cell) or tissue (e.g., a tumor), such as a cell or a tissue obtained from a subject having the same diagnosis as a subject from whom the test sample was obtained) known to be sensitive or resistant to ixabepilone or a pharmaceutically acceptable salt thereof).
  • a reference sample e.g., a cell (e.g., a cancer cell) or tissue (e.g., a tumor) known to be sensitive or resistant to ixabepilone or a pharmaceutical
  • a numerical value of a parameter in a test sample may be substantially similar to, or may correspond to, the numerical value of the parameter in a reference sample if the parameter values of the test and reference samples differ by, e.g., less than 30%, less than 29%, less than 28%, less than 27%, less than 26%, less than 25%, less than 24%, less than 23%, less than 22%, less than 21%, less than 20%, less than 19%, less than 18%, less than 17%, less than 16%, less than 15%, less than 14%, less than 13%, less than 12%, less than 11%, less than 10%, less than 9%, less than 8%, less than 7%, less than 6%, less than 5%, less than 4%, less than 3%, less than 2%, or less than 1%.
  • “Substantially dissimilar,” as used herein with respect to a numerical value of a parameter of one or more of the biomarker(s) of sensitivity and/or resistance e.g., biomarker expression level, difference score, or mean score
  • a test sample e.g., a tumor biopsy
  • a reference sample e.g., a cell (e.g., a cancer cell) or tissue (e.g., a tumor), such as a cell or a tissue obtained from a subject having the same diagnosis as a subject from whom the test sample was obtained
  • a reference sample e.g., a cell (e.g., a cancer cell) or tissue (e.g., a tumor), such as a cell or a tissue obtained from a subject having the same diagnosis as a subject from whom the test sample was obtained
  • a numerical value of a parameter in a test sample may be substantially dissimilar to the numerical value of the parameter in a reference sample if the parameter values of the test and reference samples differ by, e.g., greater than 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100% or more.
  • Treatment refers to administering or exposing a patient (e.g., a human) with a cancer (e.g., breast cancer), a cancer cell, or a tumorto an anti-cancer agent (e.g., a drug, a protein, an antibody, a nucleic acid, a chemotherapeutic agent, or a radioactive agent), or to some other form of medical intervention used to treat or prevent a disease, disorder, or condition (e.g., surgery, cryotherapy, radiation therapy, or combinations thereof).
  • a medical treatment can include ixabepilone or a pharmaceutically acceptable salt thereof.
  • the cancer to be treated is a hematological cancer or a solid tumor.
  • cancer include, e.g., breast cancer (e.g., medullary carcinoma), myeloma (e.g., multiple myeloma), colorectal cancer (e.g., colon cancer and rectal cancer), leukemia (e.g., acute myeloid leukemia, acute lymphoid leukemia, chronic myeloid leukemia, chronic lymphocytic leukemia, acute myeloblastic leukemia, acute promyelocytic leukemia, acute myelomonocytic leukemia, acute monocytic leukemia, acute erythroleukemia, and chronic leukemia), myelodysplastic syndrome, lymphoma (e.g., diffuse large B-cell lymphoma, cutaneous T-cell lymphoma, peripheral T-cell lymphoma, Hodgkin’s lymphoma, non- Hodgkin’s lymphomo
  • Radiation therapy includes the administration of a radioactive agent to a patient or exposure of a patient to radiation.
  • the radiation may be generated from sources such as particle accelerators and related medical devices or agents that emit, e.g., X-radiation, gamma radiation, or electron (Beta radiation) beams.
  • a treatment may be or further include surgery, e.g., to remove a tumor from a subject or living organism.
  • Figure 1 is a graph showing predicted ixabepilone sensitivity in pre-treatment biopsy samples from breast cancer patients later treated neoadjuvantly with ixabepilone as part of a clinical trial.
  • Patients with pathological complete remission (pCR) are predicted to be more sensitive to ixabepilone than patients with no pCR (No_pCR).
  • Figure 2 is a graph showing ixabepilone response rate (% pCR) as a function of DRP score cutoff.
  • a device such as a microarray, with one or more single-stranded oligonucleotide probes that have substantial identity (e.g., at least 85%, 90%, 95%, 99%, or 100% sequence identity) to a sequence that is complementary or identical to the nucleic acid sequence of one or more (e.g., all) biomarkers shown in Tables 1 and/or 2 can be used according to the method described herein to assess the responsiveness of a cancer patient to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • the probes can be used to detect one or more (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all) of the biomarkers of sensitivity listed in Table 1 , such as HLA-DRA (SEQ ID NO: 1), in a sample (e.g., a tumor sample) from a patient having cancer.
  • the probes can be used to detect one or more (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all) of the biomarkers of resistance listed in Table 2, such as PLK2 (SEQ ID NO: 47), in a sample (e.g., a tumor sample) from a patient having cancer.
  • the invention features individual biomarkers (e.g., HLA-DRA (SEQ ID NO: 1) or PLK2 (SEQ ID NO: 47)) and sets of biomarkers shown in Tables 1 and/or 2 that can be used to determine the responsiveness of a cancer patient to ixabepilone or a pharmaceutically acceptable salt thereof at various stages of disease progression (e.g., patients diagnosed with cancer or patients after cancer recurrence) and at different times during the treatment process (e.g., prior to administration of any cancer treatment, after administration of one or more cancer treatments other than ixabepilone or a pharmaceutically acceptable salt thereof, prior to administration of ixabepilone or a pharmaceutically acceptable salt thereof, or during administration of ixabepilone or a pharmaceutically acceptable salt thereof).
  • HLA-DRA SEQ ID NO: 1
  • PLK2 SEQ ID NO: 47
  • biomarkers of sensitivity and resistance to ixabepilone are described in detail in Tables 1 and 2, respectively, below. Table 1. mRNA biomarkers of sensitivity to ixabepilone.
  • Affymetrix IDs refer to the array type HG-U133_Plus_2. Sequences are representative probes from a probeset of typically 11 probe sequences. More than one probeset can target the same gene.
  • HLA-DRA is targeted by two different probesets (SEQ ID NOs: 1 and 2)
  • HLA-DPA1 is targeted by two different probesets (SEQ ID NOs: 10 and 12)
  • MEF2C is targeted by two different probesets (SEQ ID NOs: 19 and 24)
  • GTF3A is targeted by two different probesets (SEQ ID NOs: 33 and 37).
  • Affymetrix IDs refer to the array type HG-U133_Plus_2. Sequences are representative probes from a probeset of typically 11 probe sequences. More than one probeset can target the same gene.
  • RRAS2 is targeted by two different probesets (SEQ ID NOs: 49 and 50)
  • PTRF is targeted by two different probesets (SEQ ID NOs: 55 and 82)
  • ACTN1 is targeted by two different probesets (SEQ ID NOs: 59 and 61)
  • NNMT is targeted by two different probesets (SEQ ID NOs: 64 and 66)
  • BIN1 is targeted by three different probesets (SEQ ID NOs: 91 , 99, and 132)
  • GPRC5A is targeted by two different probesets (SEQ ID NOs: 117 and 166)
  • LAPTM4B is targeted by two different probesets (SEQ ID NOs: 124 and 159)
  • CD24 is targeted by fourdifferent probesets (SEQ ID NOs: 134, 135, 144, and 157)
  • CAV2 is targeted by two different probesets (SEQ ID NOs: 153 and 187)
  • NR2F2 is targeted by two
  • a patient may be responsive to ixabepilone or a pharmaceutically acceptable salt thereof by, e.g., detecting the expression level (e.g., mRNA or protein expression level) of one or more of the biomarkers shown in Table(s) 1 and/or 2 (e.g., HLA-DRA (SEQ ID NO: 1) and/or PLK2 (SEQ ID NO: 47)) in a biological sample (e.g., a tumor biopsy, such as, e.g., a breast cancer tumor biopsy) obtained from the subject using a device (e.g., a microarray).
  • a biological sample e.g., a tumor biopsy, such as, e.g., a breast cancer tumor biopsy
  • a device e.g., a microarray
  • the expression level of one or more of the biomarkers of sensitivity may then be compared to the expression level of the biomarker(s) in a cell or tissue (e.g., a tumor tissue) known to be sensitive or resistant to ixabepilone or a pharmaceutically acceptable salt thereof (e.g., a tumor sample from a reference subject having the same diagnosis as the patient and that has been determined to be sensitive or resistant to ixabepilone or a pharmaceutically acceptable salt thereof) to determine the patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell or tissue e.g., a tumor tissue
  • ixabepilone or a pharmaceutically acceptable salt thereof e.g., a tumor sample from a reference subject having the same diagnosis as the patient and that has been determined to be sensitive or resistant to ixabepilone or a pharmaceutically acceptable salt thereof
  • the patient may be deemed responsive to ixabepilone or a pharmaceutically acceptable salt thereof if the expression level of the one or more biomarkers of sensitivity (e.g., one or more of HLA-DRA (SEQ ID NOs: 1 and 2), ICAM3 (SEQ ID NO: 3), ITGB7 (SEQ ID NO: 4), CD8B (SEQ ID NO: 5), CD74 (SEQ ID NO: 6), HLA-DRB1 HLA-DRB4 HLA-DRB5 LOC100507709 LOC100507714 (SEQ ID NO: 7), IGJ (SEQ ID NO: 8), HLA-DRB1 HLA-DRB3 HLA-DRB4 LOC100507709 LOC100507714 (SEQ ID NO: 9), HLA-DPA1 (SEQ ID NOs: 10 and 12), HLA-DRB1 LOC100507709 LOC100507714 (SEQ ID NO: 11), CD28 (SEQ ID NO: 13), CD37 (SEQ ID
  • a patient may be deemed sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the expression level of the biomarker(s) of sensitivity in a sample is above a cutoff value of the 50 th percentile or greater (e.g., 60 th percentile, 70 th percentile, 80 th percentile, or 90 th percentile, or greater) in a cell or tissue (e.g., a tumor tissue) obtained from a reference subject in a reference population known to be responsive to ixabepilone and having the same diagnosis as the patient.
  • a cutoff value of the 50 th percentile or greater e.g., 60 th percentile, 70 th percentile, 80 th percentile, or 90 th percentile, or greater
  • a cell or tissue e.g., a tumor tissue
  • the patient may also be deemed responsive to ixabepilone or a pharmaceutically acceptable salt thereof if the level of expression of one or more of the biomarkers of resistance (e.g., one or more of PLK2 (SEQ ID NO: 47), PLXNB2 (SEQ ID NO: 48), RRAS2 (SEQ ID NO: 49 and 50), PTPLA (SEQ ID NO: 51), P2RX5-TAX1 BP3 TAX1BP3 (SEQ ID NO: 52), STAT3 (SEQ ID NO: 53), PPIC (SEQ ID NO: 54), PTRF (SEQ ID NO: 55), RCN1 (SEQ ID NO: 56), ZFP36L1 (SEQ ID NO: 57), GFPT1 (SEQ ID NO: 58 and 112), ACTN1 (SEQ ID NOs: 59 and 61), SEPT10 (SEQ ID NO: 60), COL4A1 (SEQ ID NO: 62), ERBB2IP (SEQ ID NO:
  • LGALS3BP (SEQ ID NO: 172), PLOD2 (SEQ ID NO: 173), MPZL1 (SEQ ID NO: 174), RND3 (SEQ ID NO: 175), FZD6 (SEQ ID NO: 176), LIF (SEQ ID NO: 177), TNFRSF1 A (SEQ ID NO: 178), AURKA (SEQ ID NO: 179), NR2F2 (SEQ ID NOs: 180 and 186), COPB1 (SEQ ID NO: 181), CD44 (SEQ ID NOs: 182 and 193), SMAD3 (SEQ ID NO: 183), CLPTM1 (SEQ ID NO: 184), LPHN2 (SEQ ID NO: 185), SGCE (SEQ ID NO: 188), FAM134B (SEQ ID NO: 189), IL6 (SEQ ID NO: 190), RAB32 (SEQ ID NO: 191), and FLNB (SEQ ID NO: 192)) is substantially similar to the expression level of
  • the patient may also be deemed responsive to ixabepilone or a pharmaceutically acceptable salt thereof if the level of expression of one or more of the biomarkers of sensitivity is substantially dissimilar to the expression level of the biomarker(s) of sensitivity in a cell (e.g., a cancer cell) or tissue (e.g., a tumor) known to be resistant to ixabepilone or a pharmaceutically acceptable salt thereof (e.g., a tumor sample from a reference subject having the same diagnosis as the patient and that has been determined to be resistant to ixabepilone or a pharmaceutically acceptable salt thereof).
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor
  • a pharmaceutically acceptable salt thereof e.g., a tumor sample from a reference subject having the same diagnosis as the patient and that has been determined to be resistant to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the patient may be deemed responsive to ixabepilone or a pharmaceutically acceptable salt thereof if the level of expression of one or more of the biomarkers of resistance is substantially dissimilar to the expression level of the biomarker(s) of resistance in a cell or tissue (e.g., a tumor tissue) known to be resistant to ixabepilone or a pharmaceutically acceptable salt thereof (e.g., a tumor sample from a reference subject having the same diagnosis as the patient and that has been determined to be resistant to ixabepilone or a pharmaceutically acceptable salt thereof).
  • a cell or tissue e.g., a tumor tissue
  • a pharmaceutically acceptable salt thereof e.g., a tumor sample from a reference subject having the same diagnosis as the patient and that has been determined to be resistant to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a patient may be deemed sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the expression level of the biomarker(s) of resistance in a cell is below a cutoff value of the 50 th percentile or less (e.g., 40 th percentile, 30 th percentile, 20 th percentile, or 100 th percentile, or less) in a cell or tissue (e.g., a tumor tissue) obtained from a reference subject in a reference population known to be resistant to ixabepilone and having the same diagnosis as the patient,
  • a cutoff value of the 50 th percentile or less e.g., 40 th percentile, 30 th percentile, 20 th percentile, or 100 th percentile, or less
  • tissue e.g., a tumor tissue
  • Also featured are methods of treating a patient with a cancer e.g., a patient diagnosed as having breast cancer
  • a cancer e.g., a patient diagnosed as having breast cancer
  • a cancer e.g., a patient diagnosed as having breast cancer
  • a sample e.g., a tumor sample
  • administering ixabepilone or a pharmaceutically acceptable salt thereof based on the expression levels of the biomarker(s).
  • a patient with a cancer may be administered ixabepilone or a pharmaceutically acceptable salt thereof if the expression level of one or more biomarkers of sensitivity is substantially similar to the expression level of the biomarker(s) of sensitivity in a cell or tissue (e.g., a tumor tissue) known to be sensitive to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell or tissue e.g., a tumor tissue
  • a patient with a cancer may be administered ixabepilone or a pharmaceutically acceptable salt thereof if the expression level of one or more biomarkers of resistance is substantially similar to the expression level of the biomarker(s) of resistance in a cell or tissue (e.g., a tumor tissue) known to be sensitive to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell or tissue e.g., a tumor tissue
  • a patient with a cancer may be administered ixabepilone or a pharmaceutically acceptable salt thereof if the expression level of one or more biomarkers of sensitivity is substantially dissimilar to the expression level of the biomarker(s) of sensitivity in a cell or tissue (e.g., a tumor tissue) known to be resistant to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell or tissue e.g., a tumor tissue
  • a patient with a cancer may be administered ixabepilone or a pharmaceutically acceptable salt thereof if the expression level of one or more biomarkers of resistance is substantially dissimilarto the expression level of the biomarker(s) of resistance in a cell ortissue (e.g., a tumor tissue) known to be resistant to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell ortissue e.g., a tumor tissue
  • the methods can be used to treat a cancer patient predicted to be responsive to ixabepilone or a pharmaceutically acceptable salt thereof, such as a patient with, e.g., breast cancer, estrogen receptorpositive (ERpos) breast cancer, metastatic breast cancer, multiple myeloma, acute myelogenous leukemia (AML), acute lympho-blastic leukemia (ALL), chronic lymphocytic leukemia (CLL), myelodysplastic syndrome (MDS), chronic myelogenous leukemia - chronic phase (CMLCP), diffuse large B-cell lymphoma (DLBCL), cutaneous T-cell lymphoma (CTCL), peripheral T-cell lymphoma (PTCL), Hodgkin's lymphoma, hepatocellular carcinoma (HCC), cervical cancer, prostate cancer, kidney cancer, renal cell carcinoma (RCC), esophageal cancer, melanoma, glioma, pancreatic cancer, ovarian cancer, gastrointestinal stromal tumors (G
  • Methods are described herein for identifying biomarkers of drug responsiveness, detecting biomarker gene expression in a cancer patient, determining the responsiveness of a cancer patient to ixabepilone or a pharmaceutically acceptable salt thereof, and treating cancer in a patient with ixabepilone or a pharmaceutically acceptable salt thereof. Also described are devices and kits for use in these methods.
  • the methods, devices, and kits of the invention can be used for diagnosing, prognosing, monitoring, treating, and/or reducing cancer in a subject suffering from, diagnosed with, or susceptible to cancer.
  • cancers that can be diagnosed, prognosed, monitored, treated, or reduced using the methods include hematological and solid tumors.
  • cancers include, e.g., breast cancer (e.g., medullary carcinoma), colorectal cancer (e.g., colon cancer and rectal cancer), leukemia (e.g., acute myeloid leukemia, acute lymphoid leukemia, chronic myeloid leukemia, chronic lymphocytic leukemia, acute myeloblastic leukemia, acute promyelocytic leukemia, acute myelomonocytic leukemia, acute monocytic leukemia, acute erythroleukemia, and chronic leukemia), myeloma (e.g., multiple myeloma), myelodysplastic syndrome, lymphoma (e.g., diffuse large B-cell lymphoma, cutaneous T-cell lymphoma, peripheral T-cell lymphoma, Hodgkin’s lymphoma, non-Hodgkin’s lymphoma, Waldenstrom’s macroglobulinemia, and lymphocytic
  • the methods are useful for diagnosing, prognosing, monitoring, treating, or preventing, e.g., breast cancer, multiple myeloma, acute myelogenous leukemia (AML), acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia (CLL), myelodysplastic syndrome (MDS), chronic myelogenous leukemia - chronic phase (CMLCP), diffuse large B-cell lymphoma (DLBCL), cutaneous T- cell lymphoma (CTCL), peripheral T-cell lymphoma (PTCL), Hodgkin's lymphoma, hepatocellular carcinoma (HCC), cervical cancer, prostate cancer, kidney cancer, renal cell carcinoma (RCC), esophageal cancer, melanoma, glioma, pancreatic cancer, ovarian cancer, gastrointestinal stromal tumors (GIST), sarcoma, estrogen receptor-positive (ERpos) breast cancer, metastatic breast cancer, endometrial cancer, lung cancer,
  • the cancer can be a breast cancer, such as medullary carcinoma.
  • the cancer can be estrogen receptor-positive (ER pos) breast cancer.
  • the cancer can be a metastatic form of breast cancer.
  • the breast cancer can be, for example, a Stage 0, Stage I, Stage II, Stage III, or Stage IV breast cancer.
  • a cancer patient can be assessed for sensitivity or resistance to ixabepilone or a pharmaceutically acceptable salt thereof by detecting gene expression of a biomarker (e.g., one or more of the biomarkers of Tables 1 and/or 2) in a biological sample obtained from the cancer patient (e.g., a patient with the cancer, such as, e.g., breast cancer, or a recurrence thereof).
  • the biological sample can include, for example, cells, tissue (e.g., a tissue sample obtained by biopsy), blood, serum, plasma, urine, sputum, cerebrospinal fluid, lymph tissue or fluid, or pancreatic fluid.
  • the biological sample can be fresh frozen or formalin-fixed paraffin embedded (FFPE) tissue obtained from the subject, such as a tumor sample (e.g., a biopsy) from the tissue of interest (e.g., breast, lymph nodes, thymus, spleen, bone marrow, colorectal, pancreatic, cervical, prostate, bladder, lung, gastrointestinal, head, neck, or ovarian tissue).
  • FFPE formalin-fixed paraffin embedded
  • RNA samples or tissue samples may be snap frozen in liquid nitrogen until processing or fixed in formalin and embedded in paraffin.
  • RNA may be extracted using, e.g., Trizol Reagent from Invitrogen following manufacturer's instructions, and detected directly or converted to cDNA for detection.
  • RNA may be amplified using, e.g., MessageAmp kit from Ambion following manufacturer’s instructions.
  • Amplified RNA may be quantified using, e.g., HG-U133A or HG-U133_Plus2 GeneChip from Affymetrix Inc. and compatible apparatus e.g. GCS3000Dx from Affymetrix, using the manufacturer’s instructions.
  • the Affymetrix array typically contains 11 probes (also known as a probe set) specific to each gene.
  • biomarkers shown in Tables 1 and/or2 may be measured in a biological sample (e.g., a tumor sample) obtained from the cancer patient (e.g., a patient with any of the cancer types described herein, such as a patient with recurrence of cancer) using, e.g., polymerase chain reaction (PCR), reverse transcriptase PCR (RT- PCR), quantitative real-time PCR (qPCR), an array (e.g., a microarray), a genechip, pyrosequencing, nanopore sequencing, sequencing by synthesis, sequencing by expansion, single molecule real time technology, sequencing by ligation, microfluidics, infrared fluorescence, next generation sequencing (e.g., RNA-Seq techniques), Northern blots, Western blots, Southern blots, NanoString nCounter technologies (e.g., HLA-DRA (SEQ ID NO: 1) or PLK2 (SEQ ID NO: 47)) may be measured in a
  • Devices of the invention can be used for detecting the level of expression of one or more biomarkers shown in Table(s) 1 and/or 2.
  • the device may include at least one single-stranded nucleic acid (e.g., a probe) having at least 85% sequence identity (e.g., 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity) to a nucleic acid sequence that is complementary or identical to at least 5 (e.g., at least 10, at least 15, at least 20, or more) consecutive nucleotides of one or more biomarkers shown in Table(s) 1 and/or 2 (e.g., HLA-DRA (SEQ ID NO: 1) or PLK2 (SEQ ID NO: 47)), in which the at least one single-stranded nucleic acid is sufficient for the detection of the level of expression of the one or more biomarkers.
  • a probe having at least 85% sequence identity (e.g., 85%, 90%, 95%, 97%, 98%, 99%
  • the device may be used to detect the expression level of a given biomarker by specific hybridization between the single-stranded nucleic acid and the biomarker (e.g., an mRNA, genomic DNA, or non-coding RNA), a nucleic acid encoding the biomarker (e.g., an mRNA), or a complementary nucleic acid thereof.
  • the device may be, or may include, a microarray.
  • the device may also include or be used with reagents and materials for next generation sequencing (e.g., sequencing by synthesis).
  • the device may also include or be used with NanoString reagents and at least one nCounter cartridge.
  • the device may be, or include a protein array, which contains one or more protein binding moieties (e.g., proteins, antibodies, nucleic acids, aptamers, affibodies, lipids, phospholipids, small molecules, labeled variants of any of the above, and any other moieties useful for protein detection as well known in the art) capable of detectably binding to the polypeptide product(s) of one or more biomarkers shown in Table(s) 1 and/or 2.
  • protein binding moieties e.g., proteins, antibodies, nucleic acids, aptamers, affibodies, lipids, phospholipids, small molecules, labeled variants of any of the above, and any other moieties useful for protein detection as well known in the art
  • the device may have single-stranded nucleic acid molecule(s) having the sequence of or complementary to each of the biomarkers of sensitivity selected from the biomarkers of Table 1 and/or for each of the biomarkers of resistance selected from the biomarkers of Table 2 that are affixed to the device and can be used to detect the level of expression of the biomarkers, e.g., by hybridization.
  • the level of expression of the biomarkers may be determined using high-throughput expression profiling platforms, such as microarrays.
  • a microarray for use in the methods for assessing the responsiveness of a subject with cancer e.g., a patient with recurrence of cancer
  • a subject with cancer e.g., a patient with recurrence of cancer
  • a pharmaceutically acceptable salt thereof contains or is produced by generating oligonucleotide probes (e.g., DNA, cDNA, or RNA probes) capable of hybridizing to one or more biomarkers of interest (e.g., one or more of the biomarkers of Table(s) 1 and/or 2) or the complement sequences thereof.
  • Each probe can have, e.g., at least 10, 15, 20, 25, 30, or more contiguous nucleic acid residues (e.g., at least 15) that are complementary or identical to a nucleic acid sequence of a selected biomarker.
  • the probe nucleic acid sequence can also have at least 85% (e.g., 90%, 95%, 99%, or 100%) sequence identity to the nucleic acid sequence of the gene coding the biomarker (e.g., HLA- DRA (SEQ ID NO: 1 ) or PLK2 (SEQ ID NO: 47)) or the complement sequence thereof.
  • the probe sequences can be complementary to all or a portion of the nucleic acid sequence of the biomarker(s).
  • microarrays of the invention for determining ixabepilone (e.g., ixabepilone or a pharmaceutically acceptable salt thereof) responsiveness can include probes for one or more (e.g., at least 1 , 5, 10, 15, or 20 (e.g., at least the top 1 , 5, 10, 15, or 20), or more (e.g., all)) biomarkers of sensitivity shown in Table 1 , such as HLA-DRA (SEQ ID NOs: 1 and 2), ICAM3 (SEQ ID NO: 3), ITGB7 (SEQ ID NO: 4), CD8B (SEQ ID NO: 5), CD74 (SEQ ID NO: 6), HLA-DRB1 HLA-DRB4 HLA-DRB5 LOC100507709 LOC100507714 (SEQ ID NO: 7), IGJ (SEQ ID NO: 8), HLA-DRB1 HLA-DRB3 HLA- DRB4 LOC100507709 LOC100507714 (SEQ ID NO: 1
  • Microarrays of the invention for determining ixabepilone (e.g., ixabepilone or a pharmaceutically acceptable salt thereof) responsiveness can also include probes for one or more (e.g., at least 1 , 5, 10,
  • biomarkers of resistance listed in Table 2 such as PLK2 (SEQ ID NO: 47), PLXNB2 (SEQ ID NO: 48), RRAS2 (SEQ ID NO: 49 and 50), PTPLA (SEQ ID NO: 51), P2RX5-TAX1 BP3 TAX1BP3 (SEQ ID NO: 52), STAT3 (SEQ ID NO: 53), PPIC (SEQ ID NO: 54), PTRF (SEQ ID NO: 55), RCN1 (SEQ ID NO: 56), ZFP36L1 (SEQ ID NO: 57), GFPT1 (SEQ ID NO: 58 AND 112), ACTN1 (SEQ ID NOs: 59 and 61), SEPT10 (SEQ ID NO: 60), COL4A1 (SEQ ID NO: 62), ERBB2IP (SEQ ID NO: 63), NNMT (SEQ ID NO: 63), NNMT (SEQ ID NO: 59 and 61), SEPT10 (SEQ ID NO: 60),
  • FHL2 (SEQ ID NO: 71), SHC1 (SEQ ID NO: 72), SPTAN1 (SEQ ID NO: 73), CD81 (SEQ ID NO: 74), IQGAP1 (SEQ ID NO: 75), TGIF1 (SEQ ID NO: 76), PHACTR2 (SEQ ID NO: 77), COL4A2 (SEQ ID NO: 78), CEP55 (SEQ ID NO: 79), ABCC1 (SEQ ID NO: 80), PRSS23 (SEQ ID NO: 81), PTRF (SEQ ID NO: 82), TJP1 (SEQ ID NO: 83), CRK (SEQ ID NO: 84), LASP1 (SEQ ID NO: 85), PRC1 (SEQ ID NO: 86), TMEM189 TMEM189-UBE2V1 UBE2V1 (SEQ ID NO: 87), JAK1 (SEQ ID NO: 88), ACTN4 (SEQ ID NO: 89), FAM45A F
  • a microarray probe may be single-stranded or double-stranded.
  • the probe may be labeled (e.g., detectably labeled with a fluorescent molecule, dye molecule, small molecule, epitope tag, barcode sequence, polypeptide, or any other detectable molecule).
  • Probes can be detectably labeled and immobilized on a solid support to form the microarray.
  • probes can be either prefabricated and spotted to the surface or directly synthesized on to the surface (in situ) of the microarray.
  • the microarray can also be configured such that the sequence and position of each member (e.g., probe) of the array is known.
  • a selection of biomarkers whose expression correlates with an increased likelihood of responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof can be arrayed on a solid support.
  • Hybridization of a labeled probe with a particular target nucleic acid indicates that the sample from which the mRNA was derived expresses that biomarker (e.g., the biomarker of sensitivity or resistance to ixabepilone or a pharmaceutically acceptable salt thereof).
  • biomarkers e.g., 1 to 25 (e.g., the top 1 to 25) or 10 to 25 (e.g., the top 10 to 25), or at least the top 25 of the biomarkers listed in Table(s) 1 and/or 2
  • Tissue or cell samples from a cancer patient e.g., a patient having recurrence of cancer, such as, e.g., breast cancer
  • PCR polymerase chain reaction
  • PCR-based techniques may include reverse transcription PCR (RT-PCR), quantitative real-time PCR (qPCR), reverse transcription qPCR (RT-qPCR), or quantitative loop-mediated isothermal amplification (q-LAMP).
  • RT-PCR reverse transcription PCR
  • qPCR quantitative real-time PCR
  • RT-qPCR reverse transcription qPCR
  • q-LAMP quantitative loop-mediated isothermal amplification
  • the primers and probes including the target sequences shown in Table(s) 1 and/or 2, such as HLA-DRA (SEQ ID NO: 1) or PLK2 (SEQ ID NO: 47), may be used to detect the level of expression of one or more of the indicated biomarkers using PCR.
  • the methods can include one or more steps that allow determination of the levels of target mRNA in a biological sample (e.g., by simultaneously examining the levels of a comparative control mRNA sequence or “housekeeping” gene, such as an actin family member or GAPDH).
  • the primers for these PCR-based techniques may be labeled for detection according to methods known in the art.
  • the level of expression of the biomarkers shown in Table(s) 1 and/or 2, such as HLA-DRA (SEQ ID NO: 1) or PLK2 (SEQ ID NO: 47), may be determined using sequencing technologies, such as next generation sequencing platforms (e.g., RNA-Seq), as described in Mortazavi et al., Nat. Methods 5: 621- 628, 2008, hereby incorporated by reference.
  • RNA-Seq is a robust technology for monitoring expression by direct sequencing of the RNA molecules in a sample.
  • This methodology may include fragmentation of RNA to an average length of, e.g., 200 nucleotides, conversion to cDNA by random priming, and synthesis of double-stranded cDNA (e.g., using the Just cDNA DoubleStranded cDNA Synthesis Kit from Agilent Technology).
  • the cDNA may then be converted into a molecular library for sequencing by addition of sequence adapters for each library (e.g., from lllumina®/Solexa), and the resulting 50 to 100 nucleotide reads are mapped onto the genome.
  • Exemplary sequencing platforms suitable for use according to the methods include, e.g., 454 pyrosequencing, lllumina sequencing by synthesis, SOLiD sequencing, Ion Torrent sequencing, and PacBio RS sequencing.
  • the invention features diagnostic methods for the detection and screening of cancer patients (e.g., patients with cancer or a recurrence thereof) that may be responsive to ixabepilone or a pharmaceutically acceptable salt thereof using one or more of the biomarkers shown in Table(s) 1 and/or 2 (e.g., HLA-DRA (SEQ ID NO: 1) or PLK2 (SEQ ID NO: 47)).
  • the methods of the invention may be used for predicting a patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof, and optionally, treating the cancer patient throughout the progression of cancer and/or in cases of recurrence (e.g., after a first line treatment, a second line treatment, and/or a third line treatment).
  • the invention provides individual biomarkers (e.g., HLA-DRA (SEQ ID NO: 1) or PLK2 (SEQ ID NO: 47)) and sets of biomarkers (e.g., two or more of the biomarkers listed in Table(s) 1 and/or 2), the expression levels of which, as detected in a biological sample (e.g., a tumor sample, such as a biopsy) obtained from a cancer patient (e.g., a human with cancer), are indicative of responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a biological sample e.g., a tumor sample, such as a biopsy
  • a cancer patient e.g., a human with cancer
  • the biomarkers were identified using methods similar to those previously described in, e.g., Chen et al. (Mol. Cancer Ther. 11 :34-33, 2012), Wang et al.
  • GI50 growth inhibition values
  • genes with, e.g., a Pearson correlation coefficient greater than 0.25 or below -0.25 can be classified as biomarkers of sensitivity or resistance, respectively.
  • a correlation coefficient of 0.25 or greater is a statistically significant cut-off known in the art for establishing whether the expression levels of, e.g., the genes shown in Table(s) 1 and/or 2, correlate with the likelihood of cancer treatment sensitivity, such as sensitivity to ixabepilone or a pharmaceutically acceptable salt thereof, as described in van’t Veer et al. Nature 415(6871):530-536, 2002, hereby incorporated by reference.
  • genes, or means of genes, or differences between means of genes that have an expression level above a cutoff value of the 50 th percentile or greater (e.g., 60 th percentile, 70 th percentile, 80 th percentile, or 90 th percentile, or greater) in a reference population with the same diagnosis as the patient (e.g., the same type of cancer) indicates that the sample, such as, e.g., a tumor sample (or the subject from whom the sample was taken), is predicted to be responsive (e.g., based on the biomarkers of sensitivity) or non- responsive (e.g., based on the biomarkers of resistance), respectively, to the treatment, e.g., treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • One or more biomarkers of sensitivity and/or resistance can be used to predict responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof by measuring the level of expression of the biomarker(s) in a biological sample obtained from the cancer patient.
  • a single biomarker e.g., any of the biomarkers of Table 1 or 2, such as HLA-DRA (SEQ ID NO: 1) or PLK2 (SEQ ID NO: 47)
  • a set of biomarkers e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers of Tables 1 and/or 2 (e.g., the top one, the top two, the top three, the top four, the top five, the top ten, the top fifteen, the top twenty, the top twenty five, or all of the biomarkers of Tables 1 and/or 2)
  • a cancer patient e.g., a patient with cancer recurrence
  • ixabepilone e.g., a pharmaceutically acceptable salt thereof.
  • the level of expression of the biomarker(s) in the sample may be compared to the level of expression of the biomarker(s) in a cell (e.g., a cancer cell) ortissue (e.g., a tumor tissue, such as the same type of tumor as that of the cancer patient) known to be sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue, such as the same type of tumor as that of the cancer patient
  • the level of expression of the biomarker(s) in the sample from the cancer patient is substantially similar to the expression level of the biomarker(s) in the cell ortissue (e.g., tumor tissue) known to be sensitive to ixabepilone or a pharmaceutically acceptable salt thereof, then the cancer patient is predicted to be responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • the cell ortissue e.g., tumor tissue
  • the expression level of the biomarker(s) in the sample from the cancer patient is substantially dissimilar to the expression level of the biomarker(s) in the cell ortissue (e.g., tumor tissue) known to be sensitive to ixabepilone or a pharmaceutically acceptable salt thereof, then the cancer patient is predicted to be non-responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • the cell ortissue e.g., tumor tissue
  • the expression level of the biomarker(s) in a sample from the cancer patient may also be compared to the expression level of the biomarker(s) in a cell (e.g., a cancer cell) ortissue (e.g., a tumor tissue, such as the same type of tumor as that of the cancer patient) known to be resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue, such as the same type of tumor as that of the cancer patient
  • the expression level of the biomarker(s) in the sample from the cancer patient is substantially similar to the expression level of the biomarker(s) in the cell ortissue (e.g., a tumor tissue) known to be resistant to ixabepilone or a pharmaceutically acceptable salt thereof, then the cancer patient is predicted to be non-responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • the cell ortissue e.g., a tumor tissue
  • the expression level of the biomarker(s) in the sample from the cancer patient is substantially dissimilar to the expression level of the biomarker(s) in the cell ortissue (e.g., a tumor tissue) known to be resistant to ixabepilone or a pharmaceutically acceptable salt thereof, then the cancer patient is predicted to be responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • the cell ortissue e.g., a tumor tissue
  • the responsiveness of a cancer patient (e.g., a patient with cancer recurrence) to ixabepilone or a pharmaceutically acceptable salt thereof can also be predicted by comparing the expression level of a biomarker (e.g., HLA-DRA (SEQ ID NO: 1) or PLK2 (SEQ ID NO: 47)) to the expression level of the biomarker in one or more cells or tissues (e.g., from a cancer patient population, e.g., with the same cancer as that of the subject patient) known to be sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof, and one or more cells or tissues (e.g., from a cancer patient population) known to be resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a biomarker e.g., HLA-DRA (SEQ ID NO: 1) or PLK2 (SEQ ID NO: 47)
  • the patient may be responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the expression level of the biomarker(s) is substantially similar to the expression level of the biomarker(s) in a cell or tissue (e.g., a tumor tissue) known to be sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof (e.g., the same type of cell or tissue from the patient), and if the expression level of the biomarker(s) is substantially dissimilar to the expression level of the biomarker(s) in a cell or tissue (e.g., a tumor tissue) known to be resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell or tissue e.g., a tumor tissue
  • a tumor tissue e.g., a tumor tissue
  • the patient may be non- responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the expression level of the biomarker(s) is substantially similar to the expression level of the biomarker(s) in a cell or tissue (e.g., a tumor tissue) known to be resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof, and if the expression level of the biomarker(s) is substantially dissimilar to the expression level of the biomarker(s) in a cell or tissue (e.g., a tumor tissue) known to be sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell or tissue e.g., a tumor tissue
  • a tumor tissue e.g., a tumor tissue
  • biomarkers of sensitivity e.g., one or more of HLA-DRA (SEQ ID NOs: AKAP1 (SEQ ID NO: 46)
  • biomarkers of resistance e.g., one or more of PLK2 (SEQ ID NO: 47), PLXNB2 (SEQ ID NO: 48), RRAS2 (SEQ ID NO: 49 and 50
  • PTPLA SEQ ID NO: 51
  • P2RX5- TAX1BP3 TAX1 BP3 SEQ ID NO: 52
  • STAT3 SEQ ID NO: 53
  • PPIC SEQ ID NO: 54
  • PTRF SEQ ID NO: 55
  • RCN1 SEQ ID NO: 56
  • ZFP36L1 SEQ ID NO: 57
  • GFPT1 SEQ ID NO: 58 AND 112
  • ACTN1 SEQ ID NOs: 59 and 61
  • SEPT10 SEQ ID NO: 60
  • COL4A1 SEQ ID NO: 60
  • COL4A1
  • LGALS3BP (SEQ ID NO: 172), PLOD2 (SEQ ID NO: 173), MPZL1 (SEQ ID NO: 174), RND3 (SEQ ID NO: 175), FZD6 (SEQ ID NO: 176), LIF (SEQ ID NO: 177), TNFRSF1 A (SEQ ID NO: 178), AURKA (SEQ ID NO: 179), NR2F2 (SEQ ID NOs: 180 and 186), COPB1 (SEQ ID NO: 181), CD44 (SEQ ID NOs: 182 and 193), SMAD3 (SEQ ID NO: 183), CLPTM1 (SEQ ID NO: 184), LPHN2 (SEQ ID NO: 185), SGCE (SEQ ID NO: 188), FAM134B (SEQ ID NO: 189), IL6 (SEQ ID NO: 190), RAB32 (SEQ ID NO: 191), and FLNB (SEQ ID NO: 192)) may be used in combination to determine the
  • the predicted responsiveness of a cancer patient may be determined from, e.g., the difference score, which may be defined as the difference between the mean score (i.e., mean of the expression level) of the one or more biomarkers of sensitivity of Table 1 (e.g., HLA-DRA (SEQ ID NO: 1)) and the mean score (i.e., mean of the expression level) of the one or more biomarkers of resistance of Table 2 (e.g., PLK2 (SEQ ID NO: 47)).
  • the mean score i.e., mean of the expression level
  • Table 1 e.g., HLA-DRA (SEQ ID NO: 1
  • the mean score i.e., mean of the expression level of the one or more biomarkers of resistance of Table 2
  • the difference score of the cancer patient can then be compared to the difference score in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the patient may be responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the difference score is substantially similar to the difference score in a cell or tissue (e.g., a tumor tissue) known to be sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • the patient may be responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the difference score is substantially dissimilar to the difference score in a cell or tissue (e.g., a tumor tissue) known to be resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • the patient may be non-responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the difference score is substantially similar to the difference score in a cell or tissue (e.g., a tumor tissue) known to be resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • the patient may be non-responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the difference score is substantially dissimilar to the difference score in a cell or tissue (e.g., a tumor tissue) known to be sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell or tissue e.g., a tumor tissue
  • the patient may be responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the difference score is substantially similar to the difference score in a cell or tissue (e.g., a tumor tissue) known to be sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof, relative to the difference score in a cell or tissue (e.g., a tumor tissue) known to be resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell or tissue e.g., a tumor tissue
  • a tumor tissue e.g., a tumor tissue
  • the patient may be responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the difference score is substantially dissimilar to the difference score in a cell or tissue (e.g., a tumor tissue) known to be resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof, relative to the difference score in a cell or tissue (e.g., a tumor tissue) known to be sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell or tissue e.g., a tumor tissue
  • a tumor tissue e.g., a tumor tissue
  • the patient may be non- responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the difference score is substantially similar to the difference score in a cell or tissue (e.g., a tumor tissue) known to be resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof, relative to the difference score in a cell or tissue (e.g., a tumor tissue) known to be sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell or tissue e.g., a tumor tissue
  • a tumor tissue e.g., a tumor tissue
  • the patient may be non- responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the difference score is substantially dissimilar to the difference score in a cell or tissue (e.g., a tumor tissue) known to be sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof, relative to the difference score in a cell or tissue (e.g., a tumor tissue) known to be resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell or tissue e.g., a tumor tissue
  • a tumor tissue e.g., a tumor tissue
  • the cancer patient may be determined to be responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the difference score is compared to a difference score from a reference population (e.g., a score determined using a tumor sample(s) from subjects diagnosed with the same type(s) of tumor as the subject) known to be sensitive to ixabepilone, in which an expression level at the 50 th percentile of the reference population, or the 60 th percentile, or the 70 th percentile, or the 80 th percentile, or the 90 th percentile, or greater, indicates that the sample (or the subject from whom the sample was taken) is predicted to be responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a reference population e.g., a score determined using a tumor sample(s) from subjects diagnosed with the same type(s) of tumor as the subject
  • the confidence of the prediction increases as the percentile level increases (e.g., an expression level above the 90 th percentile of a reference population indicates a greater likelihood of treatment responsiveness than an expression level at the 50 th percentile; see, e.g., Figure 2).
  • an expression level in the tested sample of below the 50 th percentile of the reference population e.g., 40 th , percentile, 30 th percentile, 20 th percentile, or 10 th percentile, or below
  • known to be responsive to ixabepilone indicates that the sample (or the subject from whom the sample was taken) is predicted to be non-responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • the mean score (i.e., mean of the expression level) of the one or more biomarkers of sensitivity of Table 1 and/or the mean score (i.e., mean of the expression level) of the one or more biomarkers of resistance of Table 2 can be used to predict responsiveness of a cancer patient (e.g., a patient with cancer recurrence) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the mean score of the biomarker(s) in a sample may be compared to the mean score of the biomarker(s) in a cell (e.g., a cancer cell) ortissue (e.g., a tumortissue) known to be sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumortissue
  • the cancer patient is predicted to be responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a patient may be deemed sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the mean score of the biomarker(s) of sensitivity in a cell or tissue (e.g., a tumor tissue) is at or above a cutoff value of the 50 th percentile in a cell or tissue (e.g., the same type of cell or tissue as tested in the patient) obtained from a reference subject in a reference population known to be responsive to ixabepilone and having the same diagnosis as the patient, or greater (e.g., 50 th percentile, 60 th percentile, 70 th percentile, 80 th percentile, or 90 th percentile, or greater).
  • a cutoff value of the 50 th percentile in a cell or tissue e.g., the same type of cell or tissue as tested in the patient
  • the mean score of the biomarker(s) in the sample from the cancer patient is substantially dissimilar to the mean score of the biomarker(s) in the cell or tissue (e.g., a tumor tissue) known to be sensitive to ixabepilone or a pharmaceutically acceptable salt thereof, then the cancer patient is predicted to be non-responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • tissue e.g., a tumor tissue
  • a patient may be deemed resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the mean score of the biomarker(s) of sensitivity in a cell or tissue (e.g., a cancer cell or tumor tissue) is below a cutoff value of the 50 th percentile or less (e.g., 40 th percentile, 30 th percentile, 20 th percentile, or 10 th percentile, or less) in a cell or tissue (e.g., the same type of cell or tissue as tested in the patient) obtained from a reference subject in a reference population known to be sensitive to ixabepilone and having the same diagnosis as the patient.
  • a cutoff value of the 50 th percentile or less e.g., 40 th percentile, 30 th percentile, 20 th percentile, or 10 th percentile, or less
  • the mean score (i.e., mean of the expression level) of the one or more biomarkers of sensitivity of Table 1 and/or the mean score (i.e., mean of the expression level) of the one or more biomarkers of resistance of Table 2 in a sample from the cancer patient may also be compared to the mean score of the biomarker(s) in a cell (e.g., a cancer cell) ortissue (e.g., a tumor tissue) known to be resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the mean score of the biomarker(s) in the sample from the cancer patient is substantially similar to the mean score of the biomarker(s) in the cell ortissue (e.g., a tumor tissue) known to be resistant to ixabepilone or a pharmaceutically acceptable salt thereof, then the cancer patient is predicted to be non-responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • the cell ortissue e.g., a tumor tissue
  • the cancer patient is predicted to be responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • the responsiveness of a cancer patient (e.g., a patient with cancer recurrence) to ixabepilone or a pharmaceutically acceptable salt thereof can also be predicted by comparing the mean score (i.e., mean of the expression level) of the one or more biomarkers of sensitivity of Table 1 and/or the mean score (i.e., mean of the expression level) of the one or more biomarkers of resistance of Table 2 in a sample from the cancer patient to the mean score of the biomarker(s) in one or more cells or tissues (e.g., from a cancer patient population) known to be sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and one or more cells or tissues (e.g., from a cancer patient population) known to be resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • the mean score i.e., mean of the expression level
  • the mean score i.e., mean of the expression level
  • the mean score i.e
  • the patient may be responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the mean score of the biomarker(s) is substantially similar to the mean score of the biomarker(s) in a cell or tissue (e.g., a tumor tissue) known to be sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof, relative to the mean score in a cell or tissue (e.g., a tumor tissue) known to be resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell or tissue e.g., a tumor tissue
  • a tumor tissue e.g., a tumor tissue
  • the patient may be responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the mean score of the biomarker(s) is substantially dissimilar to the mean score of the biomarker(s) in a cell or tissue (e.g., a tumor tissue) known to be resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof, relative to the mean score in a cell or tissue (e.g., a tumor tissue) known to be sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell or tissue e.g., a tumor tissue
  • a tumor tissue e.g., a tumor tissue
  • a patient may be deemed sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the difference between the mean score of the biomarker(s) of sensitivity and the mean score of the biomarker(s) of resistance in the sample is below a cutoff value of the 50 th percentile in a cell or tissue (e.g., a tumortissue) obtained from a reference subject in a reference population known to be resistant to ixabepilone and having the same diagnosis as the patient, or less (e.g., 40 th percentile, 30 th percentile, 20 th percentile, or 10 th percentile, or less).
  • a cutoff value of the 50 th percentile in a cell or tissue e.g., a tumortissue obtained from a reference subject in a reference population known to be resistant to ixabepilone and having the same diagnosis as the patient, or less (e.g., 40 th percentile, 30 th percentile, 20 th percentile, or 10
  • the patient may be non-responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the mean score of the biomarker(s) is substantially similar to the mean score of the biomarker(s) in a cell or tissue (e.g., a tumor tissue) known to be resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof, relative to the mean score in a cell or tissue (e.g., a tumortissue) known to be sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell or tissue e.g., a tumor tissue
  • a tumortissue e.g., a tumortissue
  • the patient may be non-responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the mean score of the biomarker(s) is substantially dissimilar to the mean score of the biomarker(s) in a cell or tissue (e.g., a tumortissue) known to be sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof, relative to the mean score in a cell or tissue (e.g., a tumortissue) known to be resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell or tissue e.g., a tumortissue
  • a tumortissue e.g., a tumortissue
  • the cancer patient may be determined to be responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the mean score (i.e., mean of the expression level) of the one or more biomarkers of sensitivity of Table 1 is compared to a mean score from a reference population (e.g., a mean score determined using a tumor sample(s) from subjects diagnosed with the same type(s) of tumor as the subject), in which an expression level at the 50 th percentile of the reference population, or the 60 th percentile, or the 70 th percentile, or the 80 th percentile, or the 90 th percentile, or greater, indicates that the sample (or the subject from whom the sample was taken) is predicted to be responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a reference population e.g., a mean score determined using a tumor sample(s) from subjects diagnosed with the same type(s) of tumor as the subject
  • the cancer patient e.g., a patient with cancer recurrence
  • the mean score i.e., mean of the expression level
  • a reference population e.g., a mean score determined using a tumor sample(s) from subjects diagnosed with the same type(s) of tumor as the subject
  • One or more biomarkers of sensitivity and/or resistance can be used to predict responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof by measuring the expression level of the biomarker(s) in a biological sample obtained from the cancer patient.
  • a single biomarker e.g., any of the biomarkers of Tables 1 and/or 2, such as (e.g., HLA-DRA (SEQ ID NO: 1) or PLK2 (SEQ ID NO: 47)
  • a set of biomarkers e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers of Tables 1 and/or2 (e.g., the top one, the top two, the top three, the top four, the top five, the top ten, the top fifteen, the top twenty, the top twenty five, or all of the biomarkers of Tables 1 and/or 2)
  • a cancer patient e.g., a patient with cancer recurrence
  • ixabepilone e.g., a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker(s) in the sample may be compared to the expression level of the biomarker(s) in a cell (e.g., a cancer cell) ortissue (e.g., a tumortissue) known to be sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumortissue
  • the expression level of the biomarker(s) in the sample from the cancer patient corresponds to the expression level of the biomarker(s) in the cell ortissue (e.g., a tumortissue) known to be sensitive to ixabepilone or a pharmaceutically acceptable salt thereof, then the cancer patient is predicted to be responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • the cell ortissue e.g., a tumortissue
  • the expression level of the biomarker(s) in the sample from the cancer patient is substantially dissimilar to the expression level of the biomarker(s) in the cell ortissue (e.g., a tumortissue) known to be sensitive to ixabepilone or a pharmaceutically acceptable salt thereof, then the cancer patient is predicted to be non-responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • the cell ortissue e.g., a tumortissue
  • the expression level of the biomarker(s) (e.g., HLA-DRA (SEQ ID NO: 1) or PLK2 (SEQ ID NO: 47)) in a sample from the cancer patient may also be compared to the expression level of the biomarker(s) in a cell (e.g., a cancer cell) ortissue (e.g., a tumortissue) known to be resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumortissue
  • the expression level of the biomarker(s) in the sample from the cancer patient corresponds to the expression level of the biomarker(s) in the cell ortissue (e.g., a tumortissue) known to be resistant to ixabepilone or a pharmaceutically acceptable salt thereof, then the cancer patient is predicted to be non-responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • the cell ortissue e.g., a tumortissue
  • the expression level of the biomarker(s) in the sample from the cancer patient is substantially dissimilar to the expression level of the biomarker(s) in the cell ortissue (e.g., a tumortissue) known to be resistant to ixabepilone or a pharmaceutically acceptable salt thereof, then the cancer patient is predicted to be responsive to treatment with ixabepilone.
  • the cell ortissue e.g., a tumortissue
  • the cancer patient is predicted to be responsive to treatment with ixabepilone.
  • the responsiveness of a cancer patient (e.g., a patient with cancer recurrence) to ixabepilone or a pharmaceutically acceptable salt thereof can also be predicted by comparing the expression level of the biomarker(s) (e.g., HLA-DRA (SEQ ID NO: 1) or PLK2 (SEQ ID NO: 47)) to the expression level of the biomarker(s) in one or more cells or tissues (e.g., from a cancer patient population, such as a cancer patient population having the same diagnosis as the cancer patient) known to be sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof, and one or more cells or tissues (e.g., from a cancer patient population, such as a cancer patient population having the same diagnosis as the cancer patient) known to be resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • the biomarker(s) e.g., HLA-DRA (SEQ ID NO: 1) or PLK2 (SEQ
  • the patient may be responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the expression level of the biomarker(s) corresponds to the expression level of the biomarker(s) in a cell or tissue (e.g., a tumor tissue) known to be sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof, relative to the expression level of the biomarker(s) in a cell or tissue (e.g., a tumor tissue) known to be resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell or tissue e.g., a tumor tissue
  • a tumor tissue e.g., a tumor tissue
  • the patient may be responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the expression level of the biomarker(s) is substantially dissimilarto the expression level of the biomarker(s) in a cell or tissue (e.g., a tumor tissue) known to be resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof, relative to the expression level of the biomarker(s) in a cell or tissue (e.g., a tumor tissue) known to be sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell or tissue e.g., a tumor tissue
  • a tumor tissue e.g., a tumor tissue
  • the patient may be non-responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the expression level of the biomarker(s) corresponds to the expression level of the biomarker(s) in a cell or tissue (e.g., a tumor tissue) known to be resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof, relative to the expression level of the biomarker(s) in a cell or tissue (e.g., a tumor tissue) known to be sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell or tissue e.g., a tumor tissue
  • a tumor tissue e.g., a tumor tissue
  • the patient may be non-responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the expression level of the biomarker(s) is substantially dissimilar to the expression level of the biomarker(s) in a cell or tissue (e.g., a tumor tissue) known to be sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof, relative to the expression level of the biomarker(s) in a cell or tissue (e.g., a tumor tissue) known to be resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell or tissue e.g., a tumor tissue
  • a tumor tissue e.g., a tumor tissue
  • biomarkers of sensitivity e.g., one or more of HLA-DRA (SEQ ID NOs:
  • ICAM3 SEQ ID NO: 3
  • ITGB7 SEQ ID NO: 4
  • CD8B SEQ ID NO: 5
  • CD74 SEQ ID NO: 6
  • HLA-DRB1 HLA-DRB4 HLA-DRB5 LOC100507709 LOC100507714 SEQ ID NO: 7
  • IGJ SEQ ID NO:
  • HLA-DRB1 HLA-DRB3 HLA-DRB4 LOC100507709 LOC100507714 (SEQ ID NO: 9), HLA-DPA1 (SEQ ID NOs: 10 and 12), HLA-DRB1 LOC100507709 LOC100507714 (SEQ ID NO: 11), CD28 (SEQ ID NO: 13), CD37 (SEQ ID NO: 14), NHP2 (SEQ ID NO: 15), MZB1 (SEQ ID NO: 16), ADCK3 (SEQ ID NO: 17), MYC (SEQ ID NO: 18), MEF2C (SEQ ID NOs: 19 and 24), RNASE6 (SEQ ID NO: 20), SRM (SEQ ID NO: 21), HAPLN1 (SEQ ID NO: 22), CYTIP (SEQ ID NO: 23), EIF3C EIF3CL (SEQ ID NO: 25), IQGAP2 (SEQ ID NO: 26), WBSCR22 (SEQ ID NO: 27), PIM2 (
  • LGALS3BP (SEQ ID NO: 172), PLOD2 (SEQ ID NO: 173), MPZL1 (SEQ ID NO: 174), RND3 (SEQ ID NO: 175), FZD6 (SEQ ID NO: 176), LIF (SEQ ID NO: 177), TNFRSF1 A (SEQ ID NO: 178), AURKA (SEQ ID NO: 179), NR2F2 (SEQ ID NOs: 180 and 186), COPB1 (SEQ ID NO: 181), CD44 (SEQ ID NOs: 182 and 193), SMAD3 (SEQ ID NO: 183), CLPTM1 (SEQ ID NO: 184), LPHN2 (SEQ ID NO: 185), SGCE (SEQ ID NO: 188), FAM134B (SEQ ID NO: 189), IL6 (SEQ ID NO: 190), RAB32 (SEQ ID NO: 191), and FLNB (SEQ ID NO: 192)) may be used in combination to determine the
  • the predicted responsiveness of a cancer patient may be determined from, e.g., the difference score, which may be defined as the difference between the mean score (i.e., mean of the expression level) of the one or more biomarkers of sensitivity of Table 1 (e.g., HLA-DRA (SEQ ID NO: 1)) and the mean score (i.e., mean of the expression level) of the one or more biomarkers of resistance of Table 2 (e.g., PLK2 (SEQ ID NO: 47)).
  • the mean score i.e., mean of the expression level
  • Table 1 e.g., HLA-DRA (SEQ ID NO: 1
  • the mean score i.e., mean of the expression level of the one or more biomarkers of resistance of Table 2
  • the difference score of the cancer patient can then be compared to the difference score in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the patient may be responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the difference score corresponds to the difference score in a cell or tissue (e.g., a tumor tissue) known to be sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • the patient may be responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the difference score is substantially dissimilar to the difference score in a cell or tissue (e.g., a tumor tissue) known to be resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • the patient may be non-responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the difference score corresponds to the difference score in a cell or tissue (e.g., a tumor tissue) known to be resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • the patient may be non-responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the difference score is substantially dissimilar to the difference score in a cell ortissue (e.g., a tumor tissue) known to be sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell ortissue e.g., a tumor tissue
  • the patient may be responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the difference score corresponds to the difference score in a cell ortissue (e.g., a tumor tissue) known to be sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof, relative to the difference score in a cell ortissue (e.g., a tumor tissue) known to be resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell ortissue e.g., a tumor tissue
  • a tumor tissue e.g., a tumor tissue
  • the patient may be responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the difference score is substantially dissimilar to the difference score in a cell ortissue (e.g., a tumor tissue) known to be resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof, relative to the difference score in a cell ortissue (e.g., a tumor tissue) known to be sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell ortissue e.g., a tumor tissue
  • a tumor tissue e.g., a tumor tissue
  • the patient may be non- responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the difference score corresponds to the difference score in a cell ortissue (e.g., a tumor tissue) known to be resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof, relative to the difference score in a cell or tissue (e.g., a tumor tissue) known to be sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell ortissue e.g., a tumor tissue
  • a tumor tissue e.g., a tumor tissue
  • the patient may be non-responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the difference score is substantially dissimilar to the difference score in a cell ortissue (e.g., a tumor tissue) known to be sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof, relative to the difference score in a cell or tissue (e.g., a tumor tissue) known to be resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell ortissue e.g., a tumor tissue
  • a tumor tissue e.g., a tumor tissue
  • the patient may be determined to be responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof if the difference score is above a cutoff value of the 50 th percentile in a reference population with the same diagnosis as the patient, or greater (e.g., the difference score is above a cutoff value of the 60 th percentile, 70 th percentile, 80 th percentile, or 90 th percentile, or greater; see, e.g., Figure 1).
  • the cell or tissue e.g., a tumor tissue
  • the cell or tissue known to be either sensitive or resistant to ixabepilone or a pharmaceutically acceptable salt thereof is of the same cancer type as the cancer patient with an unknown responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the cancer patient and the cell or tissue known to be either sensitive or resistant to ixabepilone or a pharmaceutically acceptable salt thereof may both have a cancer type selected from a hematological cancer or a solid tumor, such as, e.g., breast cancer (e.g., medullary carcinoma), myeloma (e.g., multiple myeloma), colorectal cancer (e.g., colon cancer and rectal cancer), leukemia (e.g., acute myeloid leukemia, acute lymphoid leukemia, chronic myeloid leukemia, chronic lymphocytic leukemia, acute myeloblastic leukemia, acute promyelocytic leukemia, acute myelomonocytic leukemia, acute monocytic leukemia, acute erythroleukemia, and chronic leukemia), myelodysplastic syndrome, lymphoma (e.g., diffuse large B-cell lympho
  • the cancer of the patient and the cell or tissue with known resistance or sensitivity to ixabepilone or a pharmaceutically acceptable salt thereof is, e.g., multiple myeloma, breast cancer, acute myelogenous leukemia (AML), acute lympho blastic leukemia (ALL), chronic lymphocytic leukemia (CLL), myelodysplastic syndrome (MDS), chronic myelogenous leukemia - chronic phase (CMLCP), diffuse large B-cell lymphoma (DLBCL), cutaneous T- cell lymphoma (CTCL), peripheral T-cell lymphoma (PTCL), Hodgkin's lymphoma, hepatocellular carcinoma (HCC), cervical cancer, prostate cancer, kidney cancer, renal cell carcinoma (RCC), esophageal cancer, melanoma, glioma, pancreatic cancer, ovarian cancer, gastrointestinal stromal tumors (GIST), sarcoma, breast cancer, acute myelogenous leukemia (A
  • the cancer of the patient and the cell or tissue e g., a tumor tissue
  • the cancer of the patient and the cell ortissue e.g., a tumor tissue
  • the cancer of the patient and the cell ortissue e.g., a tumor tissue
  • known resistance or sensitivity to ixabepilone or a pharmaceutically acceptable salt thereof may be a metastatic form of breast cancer.
  • the methods, devices, and kits described herein can be used to determine responsiveness of multiple types of cancer disclosed herein to ixabepilone or a pharmaceutically acceptable salt thereof.
  • Machine learning techniques such as Neural Networks, Support Vector Machines, K Nearest Neighbor, and Nearest Centroids may also be employed to develop models that discriminate patients sensitive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof from those resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof using biomarker expression as model variables, which assign each patient a classification as sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • Machine learning techniques used to classify patients using various measurements are described in U.S. Patent No. 5,822,715; U.S. Patent Application Publication Nos.
  • biomarkers of Table(s) 1 and/or 2 can be used to determine responsiveness of a cancer patient to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • the biomarker(s) of sensitivity can be selected from (a) one or more of SEQ ID NOs: 1-46 from Table 1.
  • the biomarker(s) of resistance can be selected from (a) one or more of SEQ ID NOs: 46-193 of Table 2.
  • At least one (e.g., at least 1 , at least 5, at least 10, at least 15, at least 20, at least 25, or at least 27 (e.g., at least the top 1 , at least the top 5, at least the top 10, at least the top 15, at least the top 20, at least the top 25, or at least the top 27)) of the biomarkers of sensitivity of Table 1 and/or at least one (e.g., at least 1 , at least 5, at least 10, at least 15, at least 20, at least 25, or at least 27 (e.g., at least the top 1 , at least the top 5, at least the top 10, at least the top 15, at least the top 20, at least the top 25, or at least the top 27)) of the biomarkers of resistance of Table 2 can be used to determine responsiveness of a cancer patient to treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • one biomarker of sensitivity from Table 1 e.g., HLA-DRA (SEQ ID NO: 1)
  • one biomarker of resistance from Table 2 e.g., PLK2 (SEQ ID NO: 47)
  • HLA-DRA SEQ ID NO: 1
  • PLK2 PLK2
  • the biomarker of SEQ ID NO: 1 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 1 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 1 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 1 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 1 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 2-193 to predict responsiveness of
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 2 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 2 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 2 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 2 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 2 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1 , 3-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 3 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 3 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 3 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 3 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 3 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1 , 2, 4-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 4 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 4 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 4 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 4 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 4 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-3, 5-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 5 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 5 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 5 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 5 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 5 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-4, 6-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 6 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 6 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 6 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 6 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 6 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-5, 7-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 7 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 7 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 7 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 7 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 7 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-6, 8-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 8 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 8 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 8 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 8 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 8 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-7, 9-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 9 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 9 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 9 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 9 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 9 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-8, 10-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 10 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 10 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 10 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 10 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 10 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-9, 11-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 11 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 11 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 11 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 11 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 11 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-10, 12-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 12 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 12 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 12 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 12 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 12 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-11 , 13-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 13 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 13 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 13 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 13 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 13 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-12, 14-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 14 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 14 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 14 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 14 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 14 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-13, 15-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 15 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 15 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 15 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 15 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 15 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-14, 16-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 16 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 16 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 16 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 16 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 16 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-15, 17-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 17 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 17 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 17 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 17 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 17 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-16, 18-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 18 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 18 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 18 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 18 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 18 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-17, 19-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 19 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 19 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 19 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 19 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 19 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-18, 20-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 20 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 20 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 20 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 20 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 20 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-19, 21-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 21 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 21 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 21 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 21 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 21 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-20, 22-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 22 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 22 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 22 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 22 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 22 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-21 , 23-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 23 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 23 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 23 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 23 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 23 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-22, 24-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 24 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 24 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 24 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 24 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 24 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-23, 25-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 25 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 25 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 25 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 25 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 25 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-24, 26-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 26 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 26 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 26 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 26 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 26 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-25, 27-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 27 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 27 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 27 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 27 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 27 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-26, 28-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 28 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 28 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 28 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 28 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 28 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-27, 29-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 29 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 29 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 29 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 29 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 29 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-28, 30-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 30 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 30 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 30 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 30 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 30 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-29, 31-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 31 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 31 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 31 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 31 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 31 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-30, 32-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 32 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 32 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 32 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 32 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 32 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-31 , 33-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 33 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 33 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 33 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 33 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 33 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-32, 34-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 34 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 34 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 34 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 34 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 34 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-33, 35-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 35 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 35 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 35 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 35 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 35 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-34, 36-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 36 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 36 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 36 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 36 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 36 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-35, 37-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 37 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 37 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 37 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 37 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 37 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-36, 38-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 38 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 38 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 38 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 38 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 38 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-37, 39-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 39 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 39 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 39 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 39 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 39 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-38, 40-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 40 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 40 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 40 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 40 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 40 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-39, 41-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 41 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 41 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 41 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 41 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 41 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-40, 42-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 42 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 42 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 42 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 42 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 42 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-41 , 43-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 43 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 43 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 43 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 43 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 43 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-42, 44-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 44 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 44 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 44 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 44 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 44 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-43, 45-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 45 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 45 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 45 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 45 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 45 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-44, 46-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 46 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 46 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 46 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 46 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 46 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-45, 47-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 47 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 47 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 47 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 47 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 47 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-46, 48-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 48 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 48 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 48 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 48 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 48 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-47, 49-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 49 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 49 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 49 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 49 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 49 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-48, 50-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 50 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 50 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 50 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 50 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 50 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-49, 51-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 51 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 51 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 51 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 51 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 51 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-50, 52-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 52 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 52 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 52 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 52 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 52 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-51 , 53-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 53 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 53 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 53 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 53 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 53 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-52, 54-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 54 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 54 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 54 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 54 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 54 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-53, 55-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 55 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 55 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 55 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 55 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 55 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-54, 56-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 56 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 56 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 56 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 56 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 56 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-55, 57-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 57 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 57 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 57 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 57 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 57 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-56, 58-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 58 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 58 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 58 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 58 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 58 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-57 and 59-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 59 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 59 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 59 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 59 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 59 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-58 and 60-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 60 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 60 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 60 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 60 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 60 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-59 and 61-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 61 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 61 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 61 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 61 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 61 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-60 and 62-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 62 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 62 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 62 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 62 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 62 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-61 and 63-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 63 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 63 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 63 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 63 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 63 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-62 and 64-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 64 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 64 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 64 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 64 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 64 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-63 and 65-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 65 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 65 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 65 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 65 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 65 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-64 and 66-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 65 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 65 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 65 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 65 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 65 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-64 and 66-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 66 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 66 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 66 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 66 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 66 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-65 and 67-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 67 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 67 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 67 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 67 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 67 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-66 and 68-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 68 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 68 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 68 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 68 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 68 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-67 and 69-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 69 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 69 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 69 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 69 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 69 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-68 and 70-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 70 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 70 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 70 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 70 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 70 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-69 and 71-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 71 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 71 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 71 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 71 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 71 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-70 and 72-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 72 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 72 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 72 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 72 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 72 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-71 and 72-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 73 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 73 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 73 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 73 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 73 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-72 and 74-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 74 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 74 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 74 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 74 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 74 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-73 and 75-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 75 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 75 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 75 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 75 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 75 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-74 and 76-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 76 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 76 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 76 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 76 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 76 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-75 and 77-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 77 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 77 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 77 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 77 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 77 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-76 and 78-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 78 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 78 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 78 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 78 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 78 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-77 and 79-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 79 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 79 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 79 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 79 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 79 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-78 and 80-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 80 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 80 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 80 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 80 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 80 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-79 and 81-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 81 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 81 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 81 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 81 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 81 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-80 and 82-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 82 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 82 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 82 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 82 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 82 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-81 and 83-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 83 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 83 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 83 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 83 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 83 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-82 and 84-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 84 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 84 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 84 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 84 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 84 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-83 and 85-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 85 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 85 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 85 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 85 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 85 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-84 and 86-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 86 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 86 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 86 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 86 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 86 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-85 and 87-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 87 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 87 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 87 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 87 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 87 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-86 and 88-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 88 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 88 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 88 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 88 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 88 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-87 and 89-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 89 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 89 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 89 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 89 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 89 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-88 and 90-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 90 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 90 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 90 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 90 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 90 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-89 and 91-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 91 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 91 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 91 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 91 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 91 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-90 and 92-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 92 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 92 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 92 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 92 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 92 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-91 and 93-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 93 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 93 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 93 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 93 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 93 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-92 and 94-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 94 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 94 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 94 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 94 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 94 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-93 and 95-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 95 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 95 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 95 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 95 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 95 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-94 and 96-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 96 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 96 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 96 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 96 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 96 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-95 and 97-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 97 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 97 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 97 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 97 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 97 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-96 and 98-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 98 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 98 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 98 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 98 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 98 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-97 and 99-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 99 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 99 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 99 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 99 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 99 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-98 and 100-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 100 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 100 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 100 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 100 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 100 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-99 and 101-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 101 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 101 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 101 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 101 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 101 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-100 and 102-193 to predict
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 102 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 102 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 102 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 102 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 102 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-101 and 103-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 103 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 103 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 103 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 103 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 103 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-102 and 104-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 104 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 104 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 104 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 104 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 104 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-103 and 105-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 105 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 105 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 105 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 105 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 105 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-104 and 106-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 106 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 106 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 106 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 106 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 106 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-105 and 107-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 107 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 107 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 107 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 107 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 107 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-106 and 108-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 108 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 108 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 108 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 108 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 108 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-107 and 109-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 109 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 109 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 109 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 109 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 109 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-108 and 110-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 110 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 110 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 110 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 110 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 110 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-109 and 111-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 111 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 111 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 111 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 111 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 111 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-110 and 112-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 112 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 112 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 112 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 112 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 112 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-111 and 113-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 113 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 113 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 113 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 113 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 113 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-112 and 114-19
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 114 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 114 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 114 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 114 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 114 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-113 and 115-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 115 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 115 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 115 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 115 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 115 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-114 and 116-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 116 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 116 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 116 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 116 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 116 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-115 and 117-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 117 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 117 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 117 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 117 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 117 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-116 and 118-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 118 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 118 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 118 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 118 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 118 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-117 and 119-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 119 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 119 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 119 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 119 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 119 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-118 and 120-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 120 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 120 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 120 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 120 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 120 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-119 and 121-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 121 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 121 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 121 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 121 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 121 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-120 and 122-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 122 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 122 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 122 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 122 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 122 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-121 and 123-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 123 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 123 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 123 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 123 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 123 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-122 and 124-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 124 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 124 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 124 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 124 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 124 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-123 and 125-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 125 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 125 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 125 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 125 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 125 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-124 and 126-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 126 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 126 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 126 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 126 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 126 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-125 and 127-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 127 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 127 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 127 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 127 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 127 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-126 and 128-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 128 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 128 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 128 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 128 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 128 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-127 and 129-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 129 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 129 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 129 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 129 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 129 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-128 and 130-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 130 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 130 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 130 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 130 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 130 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-129 and 131-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 131 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 131 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 131 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 131 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 131 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-130 and 132-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 132 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 132 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 132 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 132 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 132 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-131 and 133-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 133 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 133 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 133 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 133 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 133 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-132 and 134-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 134 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 134 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 134 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 134 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 134 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-133 and 135-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 135 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 135 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 135 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 135 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 135 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-134 and 136-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 136 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 136 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 136 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 136 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 136 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-135 and 137-19
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 137 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 137 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 137 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 137 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 137 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-136 and 138-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 138 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 138 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 138 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 138 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 138 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-137 and 139-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 139 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 139 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 139 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 139 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 139 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-138 and 140-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 140 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 140 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 140 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 140 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 140 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-139 and 141-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 141 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 141 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 141 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 141 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 141 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-140 and 142-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 142 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 142 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 142 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 142 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 142 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-141 and 143-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 143 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 143 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 143 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 143 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 143 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-142 and 144-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 144 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 144 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 144 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 144 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 144 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-143 and 145-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 145 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 145 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 145 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 145 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 145 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-144 and 146-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 146 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 146 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 146 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 146 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 146 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-145 and 147-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 147 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 147 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 147 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 147 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 147 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-146 and 148-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 148 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 148 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 148 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 148 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 148 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-147 and 149-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 149 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 149 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 149 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 149 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 149 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-148 and 150-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 150 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 150 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 150 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 150 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 150 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-149 and 151-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 151 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 151 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 151 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 151 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 151 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-150 and 152-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 152 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 152 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 152 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 152 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 152 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-151 and 153-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 153 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 153 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 153 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 153 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 153 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-152 and 153-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 154 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 154 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 154 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 154 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 154 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-153 and 155-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 155 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 155 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 155 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 155 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 155 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-154 and 156-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 156 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 156 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 156 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 156 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 156 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-155 and 157-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 157 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 157 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 157 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 157 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 157 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-156 and 158-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 158 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 158 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 158 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 158 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 158 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-157 and 159-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 159 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 159 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 159 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 159 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 159 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-158 and 160-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 160 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 160 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 160 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 160 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 160 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-159 and 161-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 161 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 161 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 161 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 161 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 161 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-160 and 162-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 162 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 162 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 162 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 162 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 162 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-161 and 163-19
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 163 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 163 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 163 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 163 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 163 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-162 and 164-19
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 164 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 164 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 164 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 164 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 164 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-163 and 165-19
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 165 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 165 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 165 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 165 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 165 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-164 and 166-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 166 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 166 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 166 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 166 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 166 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-165 and 167-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 167 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 167 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 167 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 167 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 167 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-166 and 168-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 168 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 168 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 168 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 168 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 168 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-167 and 169-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 169 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 169 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 169 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 169 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 169 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-168 and 170-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 170 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 170 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 170 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 170 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 170 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-169 and 171-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 171 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 171 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 171 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 171 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 171 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-170 and 172-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 172 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 172 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 172 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 172 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 172 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-171 and 173-19
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 173 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 173 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 173 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 173 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 173 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-172 and 174-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 174 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 174 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 174 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 174 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 174 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-173 and 175-19
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 175 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 175 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 175 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 175 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 175 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-174 and 176-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 176 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 176 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 176 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 176 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 176 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-175 and 177-19
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 177 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 177 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 177 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 177 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 177 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-176 and 178-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 178 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 178 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 178 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 178 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 178 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-177 and 179-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 179 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 179 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 179 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 179 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 179 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-178 and 180-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 180 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 180 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 180 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 180 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 180 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-179 and 181-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 181 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 181 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 181 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 181 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 181 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-180 and 182-193 to
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 182 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 182 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 182 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 182 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 182 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-181 and 183-19
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 183 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 183 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 183 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 183 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 183 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-182 and 184-19
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 184 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 184 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 184 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 184 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 184 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-183 and 185-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 185 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 185 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 185 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 185 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 185 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-184 and 186-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 186 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 186 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 186 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 186 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 186 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-185 and 187-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 187 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 187 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 187 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 187 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 187 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-186 and 188-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 188 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 188 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 188 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 188 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 188 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-187 and 189-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 189 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 189 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 189 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 189 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 189 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-188 and 190-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 190 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 190 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 190 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 190 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 190 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-189 and 191-193
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 191 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 191 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 191 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 191 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 191 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-190, 192, and
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 192 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 192 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 192 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 192 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 192 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-191 , and 19
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the biomarker of SEQ ID NO: 193 may be used to assess the responsiveness of a cancer patient (e.g., a patient with a cancer or a recurrence thereof) to ixabepilone or a pharmaceutically acceptable salt thereof.
  • the expression level of the biomarker of SEQ ID NO: 193 may be assessed using nucleic acid amplification methods (e.g., PCR) or a device (e.g., a microarray).
  • the expression level of the biomarker of SEQ ID NO: 193 in the patient sample may then be compared, e.g., to the expression level of the biomarker of SEQ ID NO: 193 in a cell (e.g., a cancer cell) or tissue (e.g., a tumor tissue) known to be sensitive or resistant to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and used to determine the cancer patient’s responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cell e.g., a cancer cell
  • tissue e.g., a tumor tissue
  • the biomarker of SEQ ID NO: 193 may be used alone or in combination with one or more additional biomarker(s) (e.g., one, two, three, four, five, ten, fifteen, twenty, twenty five, or all of the biomarkers shown in Tables 1 and/or 2 (e.g., the top one biomarker shown in Tables 1 and/or 2, the top two biomarker shown in Tables 1 and/or 2, the top three biomarkers shown in Tables 1 and/or 2, the top four biomarkers shown in Tables 1 and/or 2, the top five biomarkers shown in Tables 1 and/or 2, the top ten biomarkers shown in Tables 1 and/or 2, the top fifteen biomarkers shown in Tables 1 and/or 2, the top twenty biomarkers shown in Tables 1 and/or 2, the top twenty five biomarkers shown in Tables 1 and/or 2, or all of the biomarkers shown in Tables 1 and/or 2)), such as biomarker(s) of SEQ ID NOs: 1-192 to predict responsiveness of
  • the expression level of the biomarker(s) may be determined using, e.g., a microarray, PCR, or other techniques described herein, for example, using a nucleic acid probe sequence based on the target sequences shown in Tables 1 and 2.
  • the diagnostic methods of the invention permit the assessment of whether a patient is likely to be responsive to treatment with ixabepilone or a pharmaceutically acceptable salt thereof and can thus be used to direct the patient’s treatment (e.g., as a first line therapy and/or as a second or third line therapy).
  • a patient to be treated or tested for responsiveness to ixabepilone or a pharmaceutically acceptable salt thereof according to the methods may include, e.g., a patient that has been diagnosed with cancer, a patient that has not received a cancer treatment (e.g., an anti-cancer agent other than ixabepilone or a pharmaceutically acceptable salt thereof, or radiation), a patient that has received a cancer treatment (e.g., an anti-cancer agent other than ixabepilone or radiation), or a patient during treatment with ixabepilone or a pharmaceutically acceptable salt thereof.
  • a cancer treatment e.g., an anti-cancer agent other than ixabepilone or a pharmaceutically acceptable salt thereof, or radiation
  • a cancer treatment e.g., an anti-cancer agent other than ixabepilone or radiation
  • a cancer treatment e.g., an anti-cancer agent other than ixabepilone or radiation
  • the patient may have a solid tumor or a hematological cancer, such as a cancer type selected from breast cancer (e.g., medullary carcinoma), myeloma (e.g., multiple myeloma), colorectal cancer (e.g., colon cancer and rectal cancer), leukemia (e.g., acute myeloid leukemia, acute lymphoid leukemia, chronic myeloid leukemia, chronic lymphocytic leukemia, acute myeloblastic leukemia, acute promyelocytic leukemia, acute myelomonocytic leukemia, acute monocytic leukemia, acute erythroleukemia, and chronic leukemia), myelodysplastic syndrome, lymphoma (e.g., diffuse large B-cell lymphoma, cutaneous T-cell lymphoma, peripheral T-cell lymphoma, Hodgkin’s lymphoma, non-Hodgkin’s lymphoma, Walden
  • the cancer of the patient is, e.g., multiple myeloma, breast cancer, acute myelogenous leukemia (AML), acute lympho-blastic leukemia (ALL), chronic lymphocytic leukemia (CLL), myelodysplastic syndrome (MDS), chronic myelogenous leukemia - chronic phase (CMLCP), diffuse large B-cell lymphoma (DLBCL), cutaneous T-cell lymphoma (CTCL), peripheral T-cell lymphoma (PTCL), Hodgkin's lymphoma, hepatocellular carcinoma (HCC), cervical cancer, prostate cancer, kidney cancer, renal cell carcinoma (RCC), esophageal cancer, melanoma, glioma, pancreatic cancer, ovarian cancer, gastrointestinal stromal tumors (GIST), sarcoma, estrogen receptor-positive (ERpos) breast cancer, endometrial cancer, lung cancer, non-small cell lung carcinoma (NSCLC), mesotheliom

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Abstract

L'invention concerne des procédés, dispositifs, et des kits pour détecter l'expression génique chez un patient atteint d'un cancer et des procédés pour déterminer la réactivité d'un patient atteint d'un cancer à un traitement, tel qu'un traitement avec de l'ixabépilone ou un sel pharmaceutiquement acceptable de celle-ci. L'invention concerne également des procédés de traitement d'un patient atteint d'un cancer par l'administration d'un traitement, par exemple, d'un traitement avec de l'ixabépilone ou un sel pharmaceutiquement acceptable de celle-ci, en particulier lorsqu'il a été déterminé que le patient est sensible au traitement sur la base de l'expression des biomarqueurs décrits dans la description
EP21702662.4A 2020-01-31 2021-01-29 Procédés de prédiction de la réactivité à l'ixabépilone chez des patients atteints d'un cancer Pending EP4097245A1 (fr)

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US5956501A (en) 1997-01-10 1999-09-21 Health Hero Network, Inc. Disease simulation system and method
US20020006613A1 (en) 1998-01-20 2002-01-17 Shyjan Andrew W. Methods and compositions for the identification and assessment of cancer therapies
US7324926B2 (en) 1999-04-09 2008-01-29 Whitehead Institute For Biomedical Research Methods for predicting chemosensitivity or chemoresistance
AU2001245295A1 (en) 2000-02-17 2001-08-27 Millennum Pharmaceuticals, Inc. Methods and compositions for the identification, assessment, prevention and therapy of human cancers
UA75365C2 (en) 2000-08-16 2006-04-17 Bristol Myers Squibb Co Epothilone analog polymorph modifications, a method for obtaining thereof (variants), a pharmaceutical composition based thereon
US20030004338A1 (en) 2001-02-01 2003-01-02 Li Wen Sen Process for the preparation of epothilone analogs
US20050208512A1 (en) 2003-10-01 2005-09-22 The Ohio State University Research Foundation Determining the chemosensitivity of cells to cytotoxic agents
US7879545B2 (en) 2003-11-05 2011-02-01 H. Lee Moffitt Cancer Center And Research Institute, Inc. Identification of novel targets for radio sensitization using a genomic-based radiation sensitivity classifier
US20050227266A1 (en) 2004-02-06 2005-10-13 Ross Douglas T Biomarker:compound correlations in cancer diagnosis and therapy
US20110104664A1 (en) * 2006-03-31 2011-05-05 Bristol-Myers Squibb Company Biomarkers and methods for determining sensitivity to micortubule-stabilizing agents
US20110112155A1 (en) * 2008-01-15 2011-05-12 Bristol-Myers Squibb Company Methods for treating cancer in patients having breast cancer resistance protein overexpression
AU2011215753B2 (en) 2010-02-11 2015-09-03 Nanostring Technologies, Inc. Compositions and methods for the detection of small RNAs
EP2547795B1 (fr) 2010-03-16 2015-01-14 Nanostring Technologies, Inc Compositions et procédés permettant de rechercher des caractéristiques génomiques
CA2839705A1 (fr) 2011-06-24 2012-12-27 Nanostring Technologies, Inc. Dosages diagnostiques multivaries et procedes d'utilisation de ceux-ci

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